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Bioactive Molecules in SARS-CoV-2 Infection and Covid-19
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Bioactive Molecules in SARS-CoV-2 Infection and Covid-19

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Medicinal Chemistry".

Deadline for manuscript submissions: closed (31 May 2022) | Viewed by 44029

Special Issue Editors

Dr. Jean-Marc Sabatier

E-Mail Website
Guest Editor
Institute of Neurophysiopathology (INP), Aix-Marseille University, Faculté des sciences médicales et paramédicales, 27, Bd Jean Moulin, 13005 Marseille, France
Interests: antimicrobial peptides; antibacterial; antibiotics; structure-activity relationships; bacteriocins; drug design; peptide engineering
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Jacques Fantini

E-Mail Website
Guest Editor
Department of Biology, Faculty of Medicine, University of Aix-Marseille, INSERM UMR_S 1072, 13015 Marseille, France
Interests: virus-host interactions; lipid rafts; gangliosides; virus receptors; RNA viruses; SARS-CoV-2 variants; antivirals; vaccines
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues，

In this period of SARS-CoV-2 infection (and its variants) responsible for COVID-19, worldwide scientific research on coronaviruses has never been more crucial. This Special Issue of Molecules, titled ‘Bioactive Molecules in SARS-CoV-2 Infection and COVID-19’ is focused on the diverse viral and/or host molecules impacting SARS-CoV-2 and associated COVID-19 diseases. All the works dealing with detection, prevention (vaccination), and the various approaches (i.e., chemotherapeutic drugs and antibodies) to the potential treatment of coronavirus infections will be considered, with the aim to compile some key structural and functional information on SARS-CoV-2 and COVID-19. Studies on the genetic diversity of SARS-CoV-2 and its (human/animal) hosts to better understand virus transmission and distribution, viral disease progression, virus–cell interactions, molecular mechanisms, immunological aspects including ADE (antibody-dependent enhancement) and ERD (enhancement of respiratory diseases), therapy and/or vaccine efficacies, etc. are strongly invited. As guest editors, we do believe that this Special Issue will be a useful tool to virologists or researchers in the field, as well as to clinicians confronted with a growing number of patients suffering from COVID-19.

Potential contributors in the field are thus strongly encouraged to submit their work to this Special Issue. Review articles are also welcome.

Dr. Jean-Marc Sabatier
Prof. Dr. Jacques Fantini
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • SARS-CoV-2
  • COVID-19
  • renin–angiotensin system
  • angiotensin-2
  • auto-immunity
  • cytokine storm
  • ADE
  • ERD
  • ACE2 receptor
  • AT1 receptor (AT1R)
  • gangliosides
  • lipid rafts

Published Papers (6 papers)

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Research

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14 pages, 22467 KiB  
Article
Structural Dynamics of the SARS-CoV-2 Spike Protein: A 2-Year Retrospective Analysis of SARS-CoV-2 Variants (from Alpha to Omicron) Reveals an Early Divergence between Conserved and Variable Epitopes
by Patrick Guérin, Nouara Yahi, Fodil Azzaz, Henri Chahinian, Jean-Marc Sabatier and Jacques Fantini
Molecules 2022, 27(12), 3851; https://doi.org/10.3390/molecules27123851 - 15 Jun 2022
Cited by 12 | Viewed by 7903
Abstract
We analyzed the epitope evolution of the spike protein in 1,860,489 SARS-CoV-2 genomes. The structural dynamics of these epitopes was determined by molecular modeling approaches. The D614G mutation, selected in the first months of the pandemic, is still present in currently circulating SARS-CoV-2 [...] Read more.
We analyzed the epitope evolution of the spike protein in 1,860,489 SARS-CoV-2 genomes. The structural dynamics of these epitopes was determined by molecular modeling approaches. The D614G mutation, selected in the first months of the pandemic, is still present in currently circulating SARS-CoV-2 strains. This mutation facilitates the conformational change leading to the demasking of the ACE2 binding domain. D614G also abrogated the binding of facilitating antibodies to a linear epitope common to SARS-CoV-1 and SARS-CoV-2. The main neutralizing epitope of the N-terminal domain (NTD) of the spike protein showed extensive structural variability in SARS-CoV-2 variants, especially Delta and Omicron. This epitope is located on the flat surface of the NTD, a large electropositive area which binds to electronegatively charged lipid rafts of host cells. A facilitating epitope located on the lower part of the NTD appeared to be highly conserved among most SARS-CoV-2 variants, which may represent a risk of antibody-dependent enhancement (ADE). Overall, this retrospective analysis revealed an early divergence between conserved (facilitating) and variable (neutralizing) epitopes of the spike protein. These data aid in the designing of new antiviral strategies that could help to control COVID-19 infection by mimicking neutralizing antibodies or by blocking facilitating antibodies. Full article
(This article belongs to the Special Issue Bioactive Molecules in SARS-CoV-2 Infection and Covid-19)
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Review

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21 pages, 1932 KiB  
Review
The Pathophysiology of Long COVID throughout the Renin-Angiotensin System
by Shaymaa Khazaal, Julien Harb, Mohamad Rima, Cédric Annweiler, Yingliang Wu, Zhijian Cao, Ziad Abi Khattar, Christian Legros, Hervé Kovacic, Ziad Fajloun and Jean-Marc Sabatier
Molecules 2022, 27(9), 2903; https://doi.org/10.3390/molecules27092903 - 02 May 2022
Cited by 43 | Viewed by 8239
Abstract
COVID-19 has expanded across the world since its discovery in Wuhan (China) and has had a significant impact on people’s lives and health. Long COVID is a term coined by the World Health Organization (WHO) to describe a variety of persistent symptoms after [...] Read more.
COVID-19 has expanded across the world since its discovery in Wuhan (China) and has had a significant impact on people’s lives and health. Long COVID is a term coined by the World Health Organization (WHO) to describe a variety of persistent symptoms after acute SARS-CoV-2 infection. Long COVID has been demonstrated to affect various SARS-CoV-2-infected persons, independently of the acute disease severity. The symptoms of long COVID, like acute COVID-19, consist in the set of damage to various organs and systems such as the respiratory, cardiovascular, neurological, endocrine, urinary, and immune systems. Fatigue, dyspnea, cardiac abnormalities, cognitive and attention impairments, sleep disturbances, post-traumatic stress disorder, muscle pain, concentration problems, and headache were all reported as symptoms of long COVID. At the molecular level, the renin-angiotensin system (RAS) is heavily involved in the pathogenesis of this illness, much as it is in the acute phase of the viral infection. In this review, we summarize the impact of long COVID on several organs and tissues, with a special focus on the significance of the RAS in the disease pathogenesis. Long COVID risk factors and potential therapy approaches are also explored. Full article
(This article belongs to the Special Issue Bioactive Molecules in SARS-CoV-2 Infection and Covid-19)
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26 pages, 2163 KiB  
Review
Angiotensin II Type I Receptor (AT1R): The Gate towards COVID-19-Associated Diseases
by George El-Arif, Shaymaa Khazaal, Antonella Farhat, Julien Harb, Cédric Annweiler, Yingliang Wu, Zhijian Cao, Hervé Kovacic, Ziad Abi Khattar, Ziad Fajloun and Jean-Marc Sabatier
Molecules 2022, 27(7), 2048; https://doi.org/10.3390/molecules27072048 - 22 Mar 2022
Cited by 40 | Viewed by 10844
Abstract
The binding of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein to its cellular receptor, the angiotensin-converting enzyme 2 (ACE2), causes its downregulation, which subsequently leads to the dysregulation of the renin–angiotensin system (RAS) in favor of the ACE–angiotensin II (Ang [...] Read more.
The binding of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein to its cellular receptor, the angiotensin-converting enzyme 2 (ACE2), causes its downregulation, which subsequently leads to the dysregulation of the renin–angiotensin system (RAS) in favor of the ACE–angiotensin II (Ang II)–angiotensin II type I receptor (AT1R) axis. AT1R has a major role in RAS by being involved in several physiological events including blood pressure control and electrolyte balance. Following SARS-CoV-2 infection, pathogenic episodes generated by the vasoconstriction, proinflammatory, profibrotic, and prooxidative consequences of the Ang II–AT1R axis activation are accompanied by a hyperinflammatory state (cytokine storm) and an acute respiratory distress syndrome (ARDS). AT1R, a member of the G protein-coupled receptor (GPCR) family, modulates Ang II deleterious effects through the activation of multiple downstream signaling pathways, among which are MAP kinases (ERK 1/2, JNK, p38MAPK), receptor tyrosine kinases (PDGF, EGFR, insulin receptor), and nonreceptor tyrosine kinases (Src, JAK/STAT, focal adhesion kinase (FAK)), and nicotinamide adenine dinucleotide phosphate (NADPH) oxidase. COVID-19 is well known for generating respiratory symptoms, but because ACE2 is expressed in various body tissues, several extrapulmonary pathologies are also manifested, including neurologic disorders, vasculature and myocardial complications, kidney injury, gastrointestinal symptoms, hepatic injury, hyperglycemia, and dermatologic complications. Therefore, the development of drugs based on RAS blockers, such as angiotensin II receptor blockers (ARBs), that inhibit the damaging axis of the RAS cascade may become one of the most promising approaches for the treatment of COVID-19 in the near future. We herein review the general features of AT1R, with a special focus on the receptor-mediated activation of the different downstream signaling pathways leading to specific cellular responses. In addition, we provide the latest insights into the roles of AT1R in COVID-19 outcomes in different systems of the human body, as well as the role of ARBs as tentative pharmacological agents to treat COVID-19. Full article
(This article belongs to the Special Issue Bioactive Molecules in SARS-CoV-2 Infection and Covid-19)
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17 pages, 1052 KiB  
Review
The SARS-CoV-2 Entry Inhibition Mechanisms of Serine Protease Inhibitors, OM-85, Heparin and Soluble HS Might Be Linked to HS Attachment Sites
by Antony Cheudjeu
Molecules 2022, 27(6), 1947; https://doi.org/10.3390/molecules27061947 - 17 Mar 2022
Cited by 3 | Viewed by 3570
Abstract
This article discusses the importance of D-xylose for fighting viruses (especially SARS-CoV-2) that use core proteins as receptors at the cell surface, by providing additional supporting facts that these viruses probably bind at HS/CS attachment sites (i.e., the hydroxyl groups of Ser/Thr residues [...] Read more.
This article discusses the importance of D-xylose for fighting viruses (especially SARS-CoV-2) that use core proteins as receptors at the cell surface, by providing additional supporting facts that these viruses probably bind at HS/CS attachment sites (i.e., the hydroxyl groups of Ser/Thr residues of the core proteins intended to receive the D-xylose molecules to initiate the HS/CS chains). Essentially, the additional supporting facts, are: some anterior studies on the binding sites of exogenous heparin and soluble HS on the core proteins, the inhibition of the viral entry by pre-incubation of cells with heparin, and additionally, corroborating studies about the mechanism leading to type 2 diabetes during viral infection. We then discuss the mechanism by which serine protease inhibitors inhibit SARS-CoV-2 entry. The biosynthesis of heparan sulfate (HS), chondroitin sulfate (CS), dermatan sulfate (DS), and heparin (Hep) is initiated not only by D-xylose derived from uridine diphosphate (UDP)-xylose, but also bioactive D-xylose molecules, even in situations where cells were previously treated with GAG inhibitors. This property of D-xylose shown by previous anterior studies helped in the explanation of the mechanism leading to type 2 diabetes during SARS-CoV-2 infection. This explanation is completed here by a preliminary estimation of xyloside GAGs (HS/CS/DS/Hep) in the body, and with other previous studies helping to corroborate the mechanism by which the D-xylose exhibits its antiglycaemic properties and the mechanism leading to type 2 diabetes during SARS-CoV-2 infection. This paper also discusses the confirmatory studies of regarding the correlation between D-xylose and COVID-19 severity. Full article
(This article belongs to the Special Issue Bioactive Molecules in SARS-CoV-2 Infection and Covid-19)
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23 pages, 3321 KiB  
Review
Antiviral Activities of Algal-Based Sulfated Polysaccharides
by Jonathan Ardhianto Panggabean, Sya’ban Putra Adiguna, Siti Irma Rahmawati, Peni Ahmadi, Elmi Nurhaidah Zainuddin, Asep Bayu and Masteria Yunovilsa Putra
Molecules 2022, 27(4), 1178; https://doi.org/10.3390/molecules27041178 - 09 Feb 2022
Cited by 22 | Viewed by 3793
Abstract
An antiviral agent is urgently needed based on the high probability of the emergence and re-emergence of future viral disease, highlighted by the recent global COVID-19 pandemic. The emergence may be seen in the discovery of the Alpha, Beta, Gamma, Delta, and recently [...] Read more.
An antiviral agent is urgently needed based on the high probability of the emergence and re-emergence of future viral disease, highlighted by the recent global COVID-19 pandemic. The emergence may be seen in the discovery of the Alpha, Beta, Gamma, Delta, and recently discovered Omicron variants of SARS-CoV-2. The need for strategies besides testing and isolation, social distancing, and vaccine development is clear. One of the strategies includes searching for an antiviral agent that provides effective results without toxicity, which is well-presented by significant results for carrageenan nasal spray in providing efficacy against human coronavirus-infected patients. As the primary producer of sulfated polysaccharides, marine plants, including macro- and microalgae, offer versatility in culture, production, and post-isolation development in obtaining the needed antiviral agent. Therefore, this review will describe an attempt to highlight the search for practical and safe antiviral agents from algal-based sulfated polysaccharides and to unveil their features for future development. Full article
(This article belongs to the Special Issue Bioactive Molecules in SARS-CoV-2 Infection and Covid-19)
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31 pages, 9892 KiB  
Review
The Renin-Angiotensin System: A Key Role in SARS-CoV-2-Induced COVID-19
by George El-Arif, Antonella Farhat, Shaymaa Khazaal, Cédric Annweiler, Hervé Kovacic, Yingliang Wu, Zhijian Cao, Ziad Fajloun, Ziad Abi Khattar and Jean Marc Sabatier
Molecules 2021, 26(22), 6945; https://doi.org/10.3390/molecules26226945 - 17 Nov 2021
Cited by 41 | Viewed by 8026
Abstract
The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), was first identified in Eastern Asia (Wuhan, China) in December 2019. The virus then spread to Europe and across all continents where it has led to [...] Read more.
The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), was first identified in Eastern Asia (Wuhan, China) in December 2019. The virus then spread to Europe and across all continents where it has led to higher mortality and morbidity, and was declared as a pandemic by the World Health Organization (WHO) in March 2020. Recently, different vaccines have been produced and seem to be more or less effective in protecting from COVID-19. The renin–angiotensin system (RAS), an essential enzymatic cascade involved in maintaining blood pressure and electrolyte balance, is involved in the pathogenicity of COVID-19, since the angiotensin-converting enzyme II (ACE2) acts as the cellular receptor for SARS-CoV-2 in many human tissues and organs. In fact, the viral entrance promotes a downregulation of ACE2 followed by RAS balance dysregulation and an overactivation of the angiotensin II (Ang II)–angiotensin II type I receptor (AT1R) axis, which is characterized by a strong vasoconstriction and the induction of the profibrotic, proapoptotic and proinflammatory signalizations in the lungs and other organs. This mechanism features a massive cytokine storm, hypercoagulation, an acute respiratory distress syndrome (ARDS) and subsequent multiple organ damage. While all individuals are vulnerable to SARS-CoV-2, the disease outcome and severity differ among people and countries and depend on a dual interaction between the virus and the affected host. Many studies have already pointed out the importance of host genetic polymorphisms (especially in the RAS) as well as other related factors such age, gender, lifestyle and habits and underlying pathologies or comorbidities (diabetes and cardiovascular diseases) that could render individuals at higher risk of infection and pathogenicity. In this review, we explore the correlation between all these risk factors as well as how and why they could account for severe post-COVID-19 complications. Full article
(This article belongs to the Special Issue Bioactive Molecules in SARS-CoV-2 Infection and Covid-19)
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