1
|
Liu M, Liang Z, Cheng ZJ, Liu L, Liu Q, Mai Y, Chen H, Lei B, Yu S, Chen H, Zheng P, Sun B. SARS-CoV-2 neutralising antibody therapies: Recent advances and future challenges. Rev Med Virol 2023; 33:e2464. [PMID: 37322826 DOI: 10.1002/rmv.2464] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 05/01/2023] [Accepted: 05/30/2023] [Indexed: 06/17/2023]
Abstract
The COVID-19 pandemic represents an unparalleled global public health crisis. Despite concerted research endeavours, the repertoire of effective treatment options remains limited. However, neutralising-antibody-based therapies hold promise across an array of practices, encompassing the prophylaxis and management of acute infectious diseases. Presently, numerous investigations into COVID-19-neutralising antibodies are underway around the world, with some studies reaching clinical application stages. The advent of COVID-19-neutralising antibodies signifies the dawn of an innovative and promising strategy for treatment against SARS-CoV-2 variants. Comprehensively, our objective is to amalgamate contemporary understanding concerning antibodies targeting various regions, including receptor-binding domain (RBD), non-RBD, host cell targets, and cross-neutralising antibodies. Furthermore, we critically examine the prevailing scientific literature supporting neutralising antibody-based interventions, and also delve into the functional evaluation of antibodies, with a particular focus on in vitro (vivo) assays. Lastly, we identify and consider several pertinent challenges inherent to the realm of COVID-19-neutralising antibody-based treatments, offering insights into potential future directions for research and development.
Collapse
Affiliation(s)
- Mingtao Liu
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhiman Liang
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhangkai J Cheng
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Li Liu
- Guangzhou Medical University, Guangzhou, China
| | - Qiwen Liu
- Guangzhou Medical University, Guangzhou, China
| | - Yiyin Mai
- Guangzhou Medical University, Guangzhou, China
| | | | - Baoying Lei
- Guangzhou Medical University, Guangzhou, China
| | - Shangwei Yu
- Guangzhou Medical University, Guangzhou, China
| | - Huihui Chen
- Guangzhou Medical University, Guangzhou, China
| | - Peiyan Zheng
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Baoqing Sun
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| |
Collapse
|
2
|
Dong T, Wang M, Liu J, Ma P, Pang S, Liu W, Liu A. Diagnostics and analysis of SARS-CoV-2: current status, recent advances, challenges and perspectives. Chem Sci 2023; 14:6149-6206. [PMID: 37325147 PMCID: PMC10266450 DOI: 10.1039/d2sc06665c] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/03/2023] [Indexed: 06/17/2023] Open
Abstract
The disastrous spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has induced severe public healthcare issues and weakened the global economy significantly. Although SARS-CoV-2 infection is not as fatal as the initial outbreak, many infected victims suffer from long COVID. Therefore, rapid and large-scale testing is critical in managing patients and alleviating its transmission. Herein, we review the recent advances in techniques to detect SARS-CoV-2. The sensing principles are detailed together with their application domains and analytical performances. In addition, the advantages and limits of each method are discussed and analyzed. Besides molecular diagnostics and antigen and antibody tests, we also review neutralizing antibodies and emerging SARS-CoV-2 variants. Further, the characteristics of the mutational locations in the different variants with epidemiological features are summarized. Finally, the challenges and possible strategies are prospected to develop new assays to meet different diagnostic needs. Thus, this comprehensive and systematic review of SARS-CoV-2 detection technologies may provide insightful guidance and direction for developing tools for the diagnosis and analysis of SARS-CoV-2 to support public healthcare and effective long-term pandemic management and control.
Collapse
Affiliation(s)
- Tao Dong
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
- School of Pharmacy, Medical College, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Mingyang Wang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Junchong Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Pengxin Ma
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Shuang Pang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Wanjian Liu
- Qingdao Hightop Biotech Co., Ltd 369 Hedong Road, Hi-tech Industrial Development Zone Qingdao 266112 China
| | - Aihua Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| |
Collapse
|
3
|
Liu M, Gan H, Liang Z, Liu L, Liu Q, Mai Y, Chen H, Lei B, Yu S, Chen H, Zheng P, Sun B. Review of therapeutic mechanisms and applications based on SARS-CoV-2 neutralizing antibodies. Front Microbiol 2023; 14:1122868. [PMID: 37007494 PMCID: PMC10060843 DOI: 10.3389/fmicb.2023.1122868] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/23/2023] [Indexed: 03/18/2023] Open
Abstract
COVID-19 pandemic is a global public health emergency. Despite extensive research, there are still few effective treatment options available today. Neutralizing-antibody-based treatments offer a broad range of applications, including the prevention and treatment of acute infectious diseases. Hundreds of SARS-CoV-2 neutralizing antibody studies are currently underway around the world, with some already in clinical applications. The development of SARS-CoV-2 neutralizing antibody opens up a new therapeutic option for COVID-19. We intend to review our current knowledge about antibodies targeting various regions (i.e., RBD regions, non-RBD regions, host cell targets, and cross-neutralizing antibodies), as well as the current scientific evidence for neutralizing-antibody-based treatments based on convalescent plasma therapy, intravenous immunoglobulin, monoclonal antibodies, and recombinant drugs. The functional evaluation of antibodies (i.e., in vitro or in vivo assays) is also discussed. Finally, some current issues in the field of neutralizing-antibody-based therapies are highlighted.
Collapse
Affiliation(s)
- Mingtao Liu
- National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Hui Gan
- National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Zhiman Liang
- National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Li Liu
- Guangzhou Medical University, Guangzhou, China
| | - Qiwen Liu
- Guangzhou Medical University, Guangzhou, China
| | - Yiyin Mai
- Guangzhou Medical University, Guangzhou, China
| | | | - Baoying Lei
- Guangzhou Medical University, Guangzhou, China
| | - Shangwei Yu
- Guangzhou Medical University, Guangzhou, China
| | - Huihui Chen
- Guangzhou Medical University, Guangzhou, China
| | - Peiyan Zheng
- National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Baoqing Sun
- National Center for Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, China
| |
Collapse
|
4
|
Lam SD, Waman VP, Fraternali F, Orengo C, Lees J. Structural and energetic analyses of SARS-CoV-2 N-terminal domain characterise sugar binding pockets and suggest putative impacts of variants on COVID-19 transmission. Comput Struct Biotechnol J 2022; 20:6302-6316. [PMID: 36408455 PMCID: PMC9639386 DOI: 10.1016/j.csbj.2022.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 11/03/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 is an ongoing pandemic that causes significant health/socioeconomic burden. Variants of concern (VOCs) have emerged affecting transmissibility, disease severity and re-infection risk. Studies suggest that the - N-terminal domain (NTD) of the spike protein may have a role in facilitating virus entry via sialic-acid receptor binding. Furthermore, most VOCs include novel NTD variants. Despite global sequence and structure similarity, most sialic-acid binding pockets in NTD vary across coronaviruses. Our work suggests ongoing evolutionary tuning of the sugar-binding pockets and recent analyses have shown that NTD insertions in VOCs tend to lie close to loops. We extended the structural characterisation of these sugar-binding pockets and explored whether variants could enhance sialic acid-binding. We found that recent NTD insertions in VOCs (i.e., Gamma, Delta and Omicron variants) and emerging variants of interest (VOIs) (i.e., Iota, Lambda and Theta variants) frequently lie close to sugar-binding pockets. For some variants, including the recent Omicron VOC, we find increases in predicted sialic acid-binding energy, compared to the original SARS-CoV-2, which may contribute to increased transmission. These binding observations are supported by molecular dynamics simulations (MD). We examined the similarity of NTD across Betacoronaviruses to determine whether the sugar-binding pockets are sufficiently similar to be exploited in drug design. Whilst most pockets are too structurally variable, we detected a previously unknown highly structurally conserved pocket which can be investigated in pursuit of a generic pan-Betacoronavirus drug. Our structure-based analyses help rationalise the effects of VOCs and provide hypotheses for experiments. Our findings suggest a strong need for experimental monitoring of changes in NTD of VOCs.
Collapse
Affiliation(s)
- Su Datt Lam
- Institute of Structural and Molecular Biology, University College London, London, United Kingdom
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Vaishali P. Waman
- Institute of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Franca Fraternali
- Institute of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Christine Orengo
- Institute of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Jonathan Lees
- Translational Health Sciences, Bristol Medical University, University of Bristol, Bristol, United Kingdom
- Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom
| |
Collapse
|
5
|
Chen CS, Chang CN, Hu CF, Jian MJ, Chung HY, Chang CK, Perng CL, Hung KS, Chang FY, Wang CH, Chen SJ, Shang HS. Critical pediatric neurological illness associated with COVID-19 (Omicron BA.2.3.7 variant) infection in Taiwan: immunological assessment and viral genome analysis in tertiary medical center. Int J Infect Dis 2022; 124:45-48. [PMID: 36087642 PMCID: PMC9451934 DOI: 10.1016/j.ijid.2022.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/01/2022] [Accepted: 09/01/2022] [Indexed: 10/31/2022] Open
Abstract
OBJECTIVES Since April 2022, another wave of the Omicron epidemic has struck Taiwanese society, and children with severe neurological complications have been reported frequently. A few cases even developed acute fulminant encephalitis. To investigate the possible causes of the increased incidence of such complications in Taiwan, we reviewed several cases of pediatric patients with severe neurological symptoms. METHODS We collected the medical records of pediatric patients with COVID-19 infection who presented with severe neurological symptoms. The COVID-19 infection was diagnosed by nasal swab reverse transcriptase-polymerase chain reaction. The remaining samples were sent for whole genome sequencing and spike (S) protein amino acid variation mapping. RESULTS The increase of several inflammatory markers was observed in all patients included in this study. However, none of the cerebrospinal fluid samples tested positive for SARS-CoV-2. The result of whole genome sequencing showed that all the sequences belonged to the lineage BA.2.3.7. However, the sequences had a K97E mutation in the S protein that differed from other BA.2.3.7 lineage strains, which was located at the S protein N-terminal domain. CONCLUSION The new mutation in the S protein, which had not previously been observed but was discovered in this study, potentially explains the sudden increase in incidence of extremely adverse neurological symptoms in pediatric patients.
Collapse
Affiliation(s)
- Chi-Sheng Chen
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, No. 325, Sec. 2, Chenggong Rd., Neihu District, Taipei City 11490, Taiwan (R.O.C).
| | - Chia-Ning Chang
- Department of Pediatrics, Tri-Service General Hospital, National Defense Medical Center, No. 325, Sec. 2, Chenggong Rd., Neihu District, Taipei City 11490, Taiwan (R.O.C).
| | - Chih-Fen Hu
- Department of Pediatrics, Tri-Service General Hospital, National Defense Medical Center, No. 325, Sec. 2, Chenggong Rd., Neihu District, Taipei City 11490, Taiwan (R.O.C).
| | - Ming-Jr Jian
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, No. 325, Sec. 2, Chenggong Rd., Neihu District, Taipei City 11490, Taiwan (R.O.C).
| | - Hsing-Yi Chung
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, No. 325, Sec. 2, Chenggong Rd., Neihu District, Taipei City 11490, Taiwan (R.O.C).
| | - Chih-Kai Chang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, No. 325, Sec. 2, Chenggong Rd., Neihu District, Taipei City 11490, Taiwan (R.O.C).
| | - Cherng-Lih Perng
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, No. 325, Sec. 2, Chenggong Rd., Neihu District, Taipei City 11490, Taiwan (R.O.C).
| | - Kuo-Sheng Hung
- Center for Precision Medicine and Genomics, Tri-Service General Hospital, National Defense Medical Center, No. 325, Sec. 2, Chenggong Rd., Neihu District, Taipei City 11490, Taiwan (R.O.C).
| | - Feng-Yee Chang
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, No. 325, Sec. 2, Chenggong Rd., Neihu District, Taipei City 11490, Taiwan (R.O.C).
| | - Chih-Hung Wang
- Department of Otolaryngology-Head and Neck Surgery, Tri-Service General Hospital, National Defense Medical Center, No. 325, Sec. 2, Chenggong Rd., Neihu District, Taipei City 11490, Taiwan (R.O.C).
| | - Shyi-Jou Chen
- Department of Pediatrics, Tri-Service General Hospital, National Defense Medical Center, No. 325, Sec. 2, Chenggong Rd., Neihu District, Taipei City 11490, Taiwan (R.O.C).
| | - Hung-Sheng Shang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, No. 325, Sec. 2, Chenggong Rd., Neihu District, Taipei City 11490, Taiwan (R.O.C).
| |
Collapse
|
6
|
Liu XH, Cheng T, Liu BY, Chi J, Shu T, Wang T. Structures of the SARS-CoV-2 spike glycoprotein and applications for novel drug development. Front Pharmacol 2022; 13:955648. [PMID: 36016554 PMCID: PMC9395726 DOI: 10.3389/fphar.2022.955648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 07/13/2022] [Indexed: 12/14/2022] Open
Abstract
COVID-19 caused by SARS-CoV-2 has raised a health crisis worldwide. The high morbidity and mortality associated with COVID-19 and the lack of effective drugs or vaccines for SARS-CoV-2 emphasize the urgent need for standard treatment and prophylaxis of COVID-19. The receptor-binding domain (RBD) of the glycosylated spike protein (S protein) is capable of binding to human angiotensin-converting enzyme 2 (hACE2) and initiating membrane fusion and virus entry. Hence, it is rational to inhibit the RBD activity of the S protein by blocking the RBD interaction with hACE2, which makes the glycosylated S protein a potential target for designing and developing antiviral agents. In this study, the molecular features of the S protein of SARS-CoV-2 are highlighted, such as the structures, functions, and interactions of the S protein and ACE2. Additionally, computational tools developed for the treatment of COVID-19 are provided, for example, algorithms, databases, and relevant programs. Finally, recent advances in the novel development of antivirals against the S protein are summarized, including screening of natural products, drug repurposing and rational design. This study is expected to provide novel insights for the efficient discovery of promising drug candidates against the S protein and contribute to the development of broad-spectrum anti-coronavirus drugs to fight against SARS-CoV-2.
Collapse
|
7
|
Pascarella S, Bianchi M, Giovanetti M, Benvenuto D, Borsetti A, Cauda R, Cassone A, Ciccozzi M. The Biological Properties of the SARS-CoV-2 Cameroon Variant Spike: An Intermediate between the Alpha and Delta Variants. Pathogens 2022; 11:pathogens11070814. [PMID: 35890058 PMCID: PMC9315702 DOI: 10.3390/pathogens11070814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/08/2022] [Accepted: 07/18/2022] [Indexed: 02/01/2023] Open
Abstract
An analysis of the structural effect of the mutations of the B.1.640.2 (IHU) Spike Receptor Binding Domain (RBD) and N-terminal Domain (NTD) is reported along with a comparison with the sister lineage B.1.640.1. and a selection of variants of concern. The effect of the mutations on the RBD–ACE2 interaction was also assessed. The structural analysis applied computational methods that are able to carry out in silico mutagenesis to calculate energy minimization and the folding energy variation consequent to residue mutations. Tools for electrostatic calculation were applied to quantify and display the protein surface electrostatic potential. Interactions at the RBD–ACE2 interface were scrutinized using computational tools that identify the interactions and predict the contribution of each interface residue to the stability of the complex. The comparison among the RBDs shows that the most evident differences between the variants is in the distribution of the surface electrostatic potential: that of B.1.640.1 is as that of the Alpha RBD, while B.1.640.2 appears to have an intermediate surface potential pattern with characteristics between those of the Alpha and Delta variants. Moreover, the B.1.640.2 Spike includes the mutation E484K that in other variants has been suggested to be involved in immune evasion. These properties may hint at the possibility that B.1.640.2 emerged with a potentially increased infectivity with respect to the sister B.1.640.1 variant, but significantly lower than that of the Delta and Omicron variants. However, the analysis of their NTD domains highlights deletions, destabilizing mutations and charge alterations that can limit the ability of the B.1.640.1 and B.1.640.2 variants to interact with cellular components, such as cell surface receptors.
Collapse
Affiliation(s)
- Stefano Pascarella
- Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Università degli Studi di Roma La Sapienza, 00185 Roma, Italy; (S.P.); (M.B.)
| | - Martina Bianchi
- Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Università degli Studi di Roma La Sapienza, 00185 Roma, Italy; (S.P.); (M.B.)
| | - Marta Giovanetti
- Laboratory of Flavivirus, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, Brazil;
- Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, 00185 Rome, Italy
| | - Domenico Benvenuto
- Faculty of Medicine, University of Campus Bio-Medico di Roma, 00185 Rome, Italy;
| | | | - Roberto Cauda
- Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Roma, Italy;
| | - Antonio Cassone
- Universita degli Studi di Siena—Sede di Arezzo, 52100 Arezzo, Italy;
| | - Massimo Ciccozzi
- Faculty of Medicine, University of Campus Bio-Medico di Roma, 00185 Rome, Italy;
- Correspondence: ; Tel.: +39-06-225411
| |
Collapse
|
8
|
Umair M, Ikram A, Rehman Z, Haider SA, Ammar M, Badar N, Ali Q, Rana MS, Salman M. Genomic diversity of SARS-CoV-2 in Pakistan during the fourth wave of pandemic. J Med Virol 2022; 94:4869-4877. [PMID: 35754094 PMCID: PMC9349642 DOI: 10.1002/jmv.27957] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/13/2022] [Accepted: 06/24/2022] [Indexed: 12/04/2022]
Abstract
The emergence of different variants of concern of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has resulted in upsurges of coronavirus disease 2019 (COVID‐19) cases around the globe. Pakistan faced the fourth wave of COVID‐19 from July to August 2021 with 314,786 cases. To understand the genomic diversity of circulating SARS‐CoV‐2 strains during the fourth wave of the pandemic in Pakistan, this study was conducted. The samples from 140 COVID‐19‐positive patients were subjected to whole‐genome sequencing using the iSeq Sequencer by Illumina. The results showed that 97% (n = 136) of isolates belonged to the delta variant while three isolates belonged to alpha and only one isolate belonged to the beta variant. Among delta variant cases, 20.5% (n = 28) isolates were showing B.1.617.2 while 23.5% (n = 25), 17.59% (n = 19), 14.81% (n = 16), and 13.89% (n = 15) of isolates were showing AY.108, AY.43 AY.127, and AY.125 lineages, respectively. Islamabad was found to be the most affected city with 65% (n = 89) of delta variant cases, followed by Karachi (17%, n = 23), and Rawalpindi (10%, n = 14). Apart from the characteristic spike mutations (T19R, L452R, T478K, P681R, and D950N) of the delta variant, the sublineages exhibited other spike mutations as E156del, G142D, T95I, A222V, G446V, K529N, N532S, Q613H, and V483A. The phylogenetic analysis revealed the introductions from Singapore, the United Kingdom, and Germany. This study highlights the circulation of delta variants (B.1.617.2 and sublineages) during the fourth wave of pandemic in Pakistan.
Collapse
Affiliation(s)
- Massab Umair
- National Institute of Health, Islamabad, Pakistan
| | - Aamer Ikram
- National Institute of Health, Islamabad, Pakistan
| | - Zaira Rehman
- National Institute of Health, Islamabad, Pakistan
| | | | | | - Nazish Badar
- National Institute of Health, Islamabad, Pakistan
| | - Qasim Ali
- National Institute of Health, Islamabad, Pakistan
| | | | | |
Collapse
|
9
|
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The global COVID-19 pandemic continues to threaten the lives of hundreds of millions of people, with a severe negative impact on the global economy. Although several COVID-19 vaccines are currently being administered, none of them is 100% effective. Moreover, SARS-CoV-2 variants remain an important worldwide public health issue. Hence, the accelerated development of efficacious antiviral agents is urgently needed. Coronavirus depends on various host cell factors for replication. An ongoing research objective is the identification of host factors that could be exploited as targets for drugs and compounds effective against SARS-CoV-2. In the present review, we discuss the molecular mechanisms of SARS-CoV-2 and related coronaviruses, focusing on the host factors or pathways involved in SARS-CoV-2 replication that have been identified by genome-wide CRISPR screening.
Collapse
Affiliation(s)
- Yu-An Kung
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Kuo-Ming Lee
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Division of Infectious Diseases, Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Huan-Jung Chiang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Sheng-Yu Huang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chung-Jung Wu
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Shin-Ru Shih
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Research Center for Chinese Herbal Medicine, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
- Research Center for Food and Cosmetic Safety, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
- Graduate Institute of Health Industry Technology, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
| |
Collapse
|
10
|
Aminpour M, Cannariato M, Preto J, Safaeeardebili ME, Moracchiato A, Doria D, Donato F, Zizzi EA, Deriu MA, Scheim DE, Santin AD, Tuszynski JA. In Silico Analysis of the Multi-Targeted Mode of Action of Ivermectin and Related Compounds. Computation 2022; 10:51. [DOI: 10.3390/computation10040051] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Some clinical studies have indicated activity of ivermectin, a macrocyclic lactone, against COVID-19, but a biological mechanism initially proposed for this anti-viral effect is not applicable at physiological concentrations. This in silico investigation explores potential modes of action of ivermectin and 14 related compounds, by which the infectivity and morbidity of the SARS-CoV-2 virus may be limited. Binding affinity computations were performed for these agents on several docking sites each for models of (1) the spike glycoprotein of the virus, (2) the CD147 receptor, which has been identified as a secondary attachment point for the virus, and (3) the alpha-7 nicotinic acetylcholine receptor (α7nAChr), an indicated point of viral penetration of neuronal tissue as well as an activation site for the cholinergic anti-inflammatory pathway controlled by the vagus nerve. Binding affinities were calculated for these multiple docking sites and binding modes of each compound. Our results indicate the high affinity of ivermectin, and even higher affinities for some of the other compounds evaluated, for all three of these molecular targets. These results suggest biological mechanisms by which ivermectin may limit the infectivity and morbidity of the SARS-CoV-2 virus and stimulate an α7nAChr-mediated anti-inflammatory pathway that could limit cytokine production by immune cells.
Collapse
|
11
|
Di Gaetano S, Pirone L, Galdadas I, Traboni S, Iadonisi A, Pedone E, Saviano M, Gervasio FL, Capasso D. Design, Synthesis, and Anticancer Activity of a Selenium-Containing Galectin-3 and Galectin-9N Inhibitor. Int J Mol Sci 2022; 23:2581. [PMID: 35269724 DOI: 10.3390/ijms23052581] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 12/24/2022] Open
Abstract
Galectins are soluble β-D-galactoside-binding proteins whose implication in cancer progression and disease outcome makes them prominent targets for therapeutic intervention. In this frame, the development of small inhibitors that block selectively the activity of galectins represents an important strategy for cancer therapy which is, however, still relatively underdeveloped. To this end, we designed here a rationally and efficiently novel diglycosylated compound, characterized by a selenoglycoside bond and the presence of a lipophilic benzyl group at both saccharide residues. The relatively high binding affinity of the new compound to the carbohydrate recognition domain of two galectins, galectin 3 and galectin 9, its good antiproliferative and anti-migration activity towards melanoma cells, as well as its anti-angiogenesis properties, pave the way for its further development as an anticancer agent.
Collapse
|
12
|
Abstract
The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus is continuously evolving, and this poses a major threat to antibody therapies and currently authorized Coronavirus Disease 2019 (COVID-19) vaccines. It is therefore of utmost importance to investigate and predict the putative mutations on the spike protein that confer immune evasion. Antibodies are key components of the human immune system’s response to SARS-CoV-2, and the spike protein is a prime target of neutralizing antibodies (nAbs) as it plays critical roles in host cell recognition, fusion, and virus entry. The potency of therapeutic antibodies and vaccines partly depends on how readily the virus can escape neutralization. Recent structural and functional studies have mapped the epitope landscape of nAbs on the spike protein, which illustrates the footprints of several nAbs and the site of escape mutations. In this review, we discuss (1) the emerging SARS-CoV-2 variants; (2) the structural basis for antibody-mediated neutralization of SARS-CoV-2 and nAb classification; and (3) identification of the RBD escape mutations for several antibodies that resist antibody binding and neutralization. These escape maps are a valuable tool to predict SARS-CoV-2 fitness, and in conjunction with the structures of the spike-nAb complex, they can be utilized to facilitate the rational design of escape-resistant antibody therapeutics and vaccines.
Collapse
|
13
|
Aminpour M, Cannariato M, Zucco A, Di Gregorio E, Israel S, Perioli A, Tucci D, Rossi F, Pionato S, Marino S, Deriu MA, Velpula KK, Tuszynski JA. Computational Study of Potential Galectin-3 Inhibitors in the Treatment of COVID-19. Biomedicines 2021; 9:1208. [PMID: 34572394 PMCID: PMC8466820 DOI: 10.3390/biomedicines9091208] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 09/08/2021] [Accepted: 09/08/2021] [Indexed: 12/27/2022] Open
Abstract
Galectin-3 is a carbohydrate-binding protein and the most studied member of the galectin family. It regulates several functions throughout the body, among which are inflammation and post-injury remodelling. Recent studies have highlighted the similarity between Galectin-3's carbohydrate recognition domain and the so-called "galectin fold" present on the N-terminal domain of the S1 sub-unit of the SARS-CoV-2 spike protein. Sialic acids binding to the N-terminal domain of the Spike protein are known to be crucial for viral entry into humans, and the role of Galectin-3 as a mediator of lung fibrosis has long been the object of study since its levels have been found to be abnormally high in alveolar macrophages following lung injury. In this context, the discovery of a double inhibitor may both prevent viral entry and reduce post-infection pulmonary fibrosis. In this study, we use a database of 56 compounds, among which 37 have known experimental affinity with Galectin-3. We carry out virtual screening of this database with respect to Galectin-3 and Spike protein. Several ligands are found to exhibit promising binding affinity and interaction with the Spike protein's N-terminal domain as well as with Galectin-3. This finding strongly suggests that existing Galectin-3 inhibitors possess dual-binding capabilities to disrupt Spike-ACE2 interactions. Herein we identify the most promising inhibitors of Galectin-3 and Spike proteins, of which five emerge as potential dual effective inhibitors. Our preliminary results warrant further in vitro and in vivo testing of these putative inhibitors against SARS-CoV-2 with the hope of being able to halt the spread of the virus in the future.
Collapse
Affiliation(s)
- Maral Aminpour
- Department of Biomedical Engineering, University of Alberta, Edmonton, AB T6G 1Z2, Canada;
| | - Marco Cannariato
- DIMEAS, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (M.C.); (A.Z.); (E.D.G.); (S.I.); (A.P.); (D.T.); (F.R.); (S.P.); (S.M.); (M.A.D.)
| | - Angelica Zucco
- DIMEAS, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (M.C.); (A.Z.); (E.D.G.); (S.I.); (A.P.); (D.T.); (F.R.); (S.P.); (S.M.); (M.A.D.)
| | - Elisabetta Di Gregorio
- DIMEAS, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (M.C.); (A.Z.); (E.D.G.); (S.I.); (A.P.); (D.T.); (F.R.); (S.P.); (S.M.); (M.A.D.)
| | - Simone Israel
- DIMEAS, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (M.C.); (A.Z.); (E.D.G.); (S.I.); (A.P.); (D.T.); (F.R.); (S.P.); (S.M.); (M.A.D.)
| | - Annalisa Perioli
- DIMEAS, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (M.C.); (A.Z.); (E.D.G.); (S.I.); (A.P.); (D.T.); (F.R.); (S.P.); (S.M.); (M.A.D.)
| | - Davide Tucci
- DIMEAS, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (M.C.); (A.Z.); (E.D.G.); (S.I.); (A.P.); (D.T.); (F.R.); (S.P.); (S.M.); (M.A.D.)
| | - Francesca Rossi
- DIMEAS, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (M.C.); (A.Z.); (E.D.G.); (S.I.); (A.P.); (D.T.); (F.R.); (S.P.); (S.M.); (M.A.D.)
| | - Sara Pionato
- DIMEAS, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (M.C.); (A.Z.); (E.D.G.); (S.I.); (A.P.); (D.T.); (F.R.); (S.P.); (S.M.); (M.A.D.)
| | - Silvia Marino
- DIMEAS, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (M.C.); (A.Z.); (E.D.G.); (S.I.); (A.P.); (D.T.); (F.R.); (S.P.); (S.M.); (M.A.D.)
| | - Marco A. Deriu
- DIMEAS, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (M.C.); (A.Z.); (E.D.G.); (S.I.); (A.P.); (D.T.); (F.R.); (S.P.); (S.M.); (M.A.D.)
| | - Kiran K. Velpula
- Department of Cancer Biology and Pharmacology, Pediatrics and Neurosurgery, University of Illinois College of Medicine at Peoria, Peoria, IL 61605, USA
| | - Jack A. Tuszynski
- DIMEAS, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (M.C.); (A.Z.); (E.D.G.); (S.I.); (A.P.); (D.T.); (F.R.); (S.P.); (S.M.); (M.A.D.)
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada
| |
Collapse
|