1
|
Queirós-Reis L, Mesquita JR, Brancale A, Bassetto M. Exploring the Fatty Acid Binding Pocket in the SARS-CoV-2 Spike Protein - Confirmed and Potential Ligands. J Chem Inf Model 2023; 63:7282-7298. [PMID: 37991468 DOI: 10.1021/acs.jcim.3c00803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Severe Acute Respiratory syndrome 2 (SARS-CoV-2) is a respiratory virus responsible for coronavirus disease 19 (COVID-19) and the still ongoing and unprecedented global pandemic. The key viral protein for cell infection is the spike glycoprotein, a surface-exposed fusion protein that both recognizes and mediates entry into host cells. Within the spike glycoprotein, a fatty acid binding pocket (FABP) was confirmed, with the crystallization of linoleic acid (LA) occupying a well-defined site. Importantly, when the pocket is occupied by a fatty acid, an inactive conformation is stabilized, and cell recognition is hindered. In this review, we discuss ligands reported so far for this site, correlating their activity predicted through in silico studies with antispike experimental activity, assessed by either binding assays or cell-infection assays. LA was the first confirmed ligand, cocrystallized in a cryo-EM structure of the spike protein, resulting in increased stability of the inactive conformation of the spike protein. The next identified ligand, lifitegrast, was also experimentally confirmed as a ligand with antiviral activity, suggesting the potential for diverse chemical scaffolds to bind this site. Finally, SPC-14 was also confirmed as a ligand, although no inhibition assays were performed. In this review, we identified 20 studies describing small-molecule compounds predicted to bind the pocket in in silico studies and with confirmed binding or in vitro activity, either inhibitory activity against the spike-ACE2 interaction or antiviral activity in cell-based assays. When considering all ligands confirmed with in vitro assays, a good overall occupation of the pocket should be complemented with the ability to make direct interactions, both hydrophilic and hydrophobic, with key amino acid residues defining the pocket surface. Among the active compounds, long flexible carbon chains are recurrent, with retinoids capable of binding the FABP, although bulkier systems are also capable of affecting viral fitness. Compounds able to bind this site with high affinity have the potential to stabilize the inactive conformation of the SARS-CoV-2 spike protein and therefore reduce the virus's ability to infect new cells. Since this pocket is conserved in highly pathogenic human coronaviruses, including MERS-CoV and SARS-CoV, this effect could be exploited for the development of new antiviral agents, with broad-spectrum anticoronavirus activity.
Collapse
Affiliation(s)
- Luís Queirós-Reis
- Abel Salazar Institute of Biomedical Sciences (ICBAS), University of Porto, 4050-313 Porto, Portugal
| | - João R Mesquita
- Abel Salazar Institute of Biomedical Sciences (ICBAS), University of Porto, 4050-313 Porto, Portugal
- Epidemiology Research Unit (EPIunit), Institute of Public Health, University of Porto, 4050-091 Porto, Portugal
| | - Andrea Brancale
- University of Chemistry and Technology, Prague, 166 28 Praha, Czechia
| | - Marcella Bassetto
- School of Pharmacy and Pharmaceutical Sciences, College of Biomedical and Life Sciences, Cardiff University, Cardiff CF10 3BN, U.K
- Department of Chemistry, Faculty of Science and Engineering, Swansea University, Swansea SA2 8PP, U.K
| |
Collapse
|
2
|
Li Q, Shah T, Wang B, Qu L, Wang R, Hou Y, Baloch Z, Xia X. Cross-species transmission, evolution and zoonotic potential of coronaviruses. Front Cell Infect Microbiol 2023; 12:1081370. [PMID: 36683695 PMCID: PMC9853062 DOI: 10.3389/fcimb.2022.1081370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/19/2022] [Indexed: 01/09/2023] Open
Abstract
Coronaviruses (CoVs) continuously evolve, crossing species barriers and spreading across host ranges. Over the last two decades, several CoVs (HCoV-229E, HCoV-NL63, HCoV-HKU1, HCoV-OC43, SARS-CoV, MERS-CoV, and SARS-CoV-2) have emerged in animals and mammals, causing significant economic and human life losses. Due to CoV cross-species transmission and the evolution of novel viruses, it is critical to identify their natural reservoiurs and the circumstances under which their transmission occurs. In this review, we use genetic and ecological data to disentangle the evolution of various CoVs in wildlife, humans, and domestic mammals. We thoroughly investigate several host species and outline the epidemiology of CoVs toward specific hosts. We also discuss the cross-species transmission of CoVs at the interface of wildlife, animals, and humans. Clarifying the epidemiology and diversity of species reservoirs will significantly impact our ability to respond to the future emergence of CoVs in humans and domestic animals.
Collapse
Affiliation(s)
- Qian Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China,The First Affiliated Hospital & Clinical Medical College, Dali University, Dali, Yunnan, China
| | - Taif Shah
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Binghui Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Linyu Qu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Rui Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Yutong Hou
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Zulqarnain Baloch
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China,*Correspondence: Xueshan Xia,
| |
Collapse
|
3
|
Mori H, Kondo E, Yoshino K. Acute Myositis in a Pregnant Woman Complicated With COVID-19 and Hyperemesis Gravidarum: A Case Report. J UOEH 2023; 45:161-165. [PMID: 37661388 DOI: 10.7888/juoeh.45.161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Myalgia is the most frequently reported neuromuscular symptom in COVID-19 patients, with a frequency of around 20% in pregnant women. Acute myositis due to COVID-19 is severe and requires medical intervention. There have been some reports of acute myositis due to COVID-19, mostly in elderly men, but rarely in pregnant women. Here we report a case of a pregnant woman who was diagnosed with acute myositis following COVID-19 illness early in her pregnancy. She had been affected by morning sickness since the 6th week of gestation and was diagnosed with COVID-19 at the 12th week. Muscle pain appeared in her limbs 5 days after the diagnosis of COVID-19, with a predominance of pain in the lower limbs, and her gait gradually became unstable. We concluded that it was acute myositis complicated by COVID-19 and hypokalemia, but we could not determine whether hypokalemia or COVID-19 or both were the cause of the muscle damage in this case. Pregnant women diagnosed with COVID-19 often complain of myalgia and fatigue, and when a pregnant woman's symptoms are severe we should keep in mind that they may be suffering from muscle damage that needs medical intervention.
Collapse
Affiliation(s)
- Hiroshi Mori
- Department of Obstetrics and Gynecology, School of Medicine, University of Occupational and Environmental health, Japan
| | - Emi Kondo
- Department of Obstetrics and Gynecology, School of Medicine, University of Occupational and Environmental health, Japan
| | - Kiyoshi Yoshino
- Department of Obstetrics and Gynecology, School of Medicine, University of Occupational and Environmental health, Japan
| |
Collapse
|
4
|
Queirós-Reis L, Gomes da Silva P, Gonçalves J, Brancale A, Bassetto M, Mesquita JR. SARS-CoV-2 Virus-Host Interaction: Currently Available Structures and Implications of Variant Emergence on Infectivity and Immune Response. Int J Mol Sci 2021; 22:10836. [PMID: 34639178 PMCID: PMC8509653 DOI: 10.3390/ijms221910836] [Citation(s) in RCA: 6] [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: 09/03/2021] [Revised: 09/24/2021] [Accepted: 10/01/2021] [Indexed: 01/11/2023] Open
Abstract
Coronavirus disease 19, or COVID-19, is an infection associated with an unprecedented worldwide pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), which has led to more than 215 million infected people and more than 4.5 million deaths worldwide. SARS-CoV-2 cell infection is initiated by a densely glycosylated spike (S) protein, a fusion protein, binding human angiotensin converting enzyme 2 (hACE2), that acts as the functional receptor through the receptor binding domain (RBD). In this article, the interaction of hACE2 with the RBD and how fusion is initiated after recognition are explored, as well as how mutations influence infectivity and immune response. Thus, we focused on all structures available in the Protein Data Bank for the interaction between SARS-CoV-2 S protein and hACE2. Specifically, the Delta variant carries particular mutations associated with increased viral fitness through decreased antibody binding, increased RBD affinity and altered protein dynamics. Combining both existing mutations and mutagenesis studies, new potential SARS-CoV-2 variants, harboring advantageous S protein mutations, may be predicted. These include mutations S13I and W152C, decreasing antibody binding, N460K, increasing RDB affinity, or Q498R, positively affecting both properties.
Collapse
Affiliation(s)
- Luís Queirós-Reis
- Abel Salazar Institute of Biomedical Sciences (ICBAS), University of Porto, 4050-313 Porto, Portugal; (L.Q.-R.); (P.G.d.S.)
| | - Priscilla Gomes da Silva
- Abel Salazar Institute of Biomedical Sciences (ICBAS), University of Porto, 4050-313 Porto, Portugal; (L.Q.-R.); (P.G.d.S.)
- Epidemiology Research Unit (EPIunit), Institute of Public Health, University of Porto, 4050-091 Porto, Portugal
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, 4200-465 Porto, Portugal
| | - José Gonçalves
- Institute of Sustainable Processes, University of Valladolid, 47011 Valladolid, Spain;
| | - Andrea Brancale
- Cardiff School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff CF10 3NB, UK;
| | - Marcella Bassetto
- Department of Chemistry, Faculty of Science and Engineering, Swansea University,
Swansea SA2 8PP, UK;
| | - João R. Mesquita
- Abel Salazar Institute of Biomedical Sciences (ICBAS), University of Porto, 4050-313 Porto, Portugal; (L.Q.-R.); (P.G.d.S.)
- Epidemiology Research Unit (EPIunit), Institute of Public Health, University of Porto, 4050-091 Porto, Portugal
| |
Collapse
|
5
|
Schoeman D, Fielding BC. Human Coronaviruses: Counteracting the Damage by Storm. Viruses 2021; 13:1457. [PMID: 34452323 PMCID: PMC8402835 DOI: 10.3390/v13081457] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/16/2021] [Accepted: 07/20/2021] [Indexed: 12/15/2022] Open
Abstract
Over the past 18 years, three highly pathogenic human (h) coronaviruses (CoVs) have caused severe outbreaks, the most recent causative agent, SARS-CoV-2, being the first to cause a pandemic. Although much progress has been made since the COVID-19 pandemic started, much about SARS-CoV-2 and its disease, COVID-19, is still poorly understood. The highly pathogenic hCoVs differ in some respects, but also share some similarities in clinical presentation, the risk factors associated with severe disease, and the characteristic immunopathology associated with the progression to severe disease. This review aims to highlight these overlapping aspects of the highly pathogenic hCoVs-SARS-CoV, MERS-CoV, and SARS-CoV-2-briefly discussing the importance of an appropriately regulated immune response; how the immune response to these highly pathogenic hCoVs might be dysregulated through interferon (IFN) inhibition, antibody-dependent enhancement (ADE), and long non-coding RNA (lncRNA); and how these could link to the ensuing cytokine storm. The treatment approaches to highly pathogenic hCoV infections are discussed and it is suggested that a greater focus be placed on T-cell vaccines that elicit a cell-mediated immune response, using rapamycin as a potential agent to improve vaccine responses in the elderly and obese, and the potential of stapled peptides as antiviral agents.
Collapse
Affiliation(s)
| | - Burtram C. Fielding
- Molecular Biology and Virology Research Laboratory, Department of Medical Biosciences, University of the Western Cape, Cape Town 7535, South Africa;
| |
Collapse
|