SARS-CoV-2 Enzymes: from Virus-Host Interactions to Identification of Innovative Therapeutic Approaches

A special issue of Catalysts (ISSN 2073-4344). This special issue belongs to the section "Biocatalysis".

Deadline for manuscript submissions: closed (20 February 2022) | Viewed by 8678

Special Issue Editors


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Guest Editor
CSIC, Instituto de Química Orgánica General, IQOG, C/ Juan de la Cierva 3, E-28006 Madrid, Spain
Interests: small biomolecules; molecular modeling; enzyme as a catalyst; combination therapy; inhibitors or decoy acceptors as drugs; carbohydrates
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Guest Editor
Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 OBP, UK
Interests: biomolecular structure; X-ray protein crystallography; cell division regulation; cell signalling; macromolecular complexes; early stage drug discovery; chemoinformatics

Special Issue Information

Dear Colleagues,

The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 constitutes the greatest public health concern of our time. A total of 29 proteins are predicted to be encoded by the SARS-CoV-2 genome. The function(s) of some of these proteins remain(s) obscure, whereas others have been established. Some of these proteins have been identified as promising targets for new small-size drugs, biological such as therapeutic antibodies and siRNA-based approaches as well as vaccine development to treat COVID-19. Undoubtedly, an enhanced understanding of the activity and potential druggability of the pool of SARS-CoV-2 enzymes is of paramount importance to ensure progress in these areas. A steady stream of recent primary research publications and review articles are testimony to the multiple efforts across the globe to tackle COVID-19. However, a more holistic account of SARS-CoV-2 enzyme function, mode of regulation, and exploitation as suitable drug targets remain an important pending assignment in the field. This research topic addresses this gap in knowledge and aims to include contributions from leading scientists with a long-standing interest in coronavirus biology, ranging from phylogenetics analysis and the study of coronavirus–host interactions, to the effect of SARS-CoV-2 enzymes in the immune response, to the discovery of specific inhibitors to suppress their biological activity.

Dr. Agatha Bastida Codina
Dr. Victor M Bolanos-Garcia
Guest Editors

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Keywords

  • SARS-CoV-2
  • coronavirus
  • COVID-19
  • antivirals
  • vaccine
  • antibody
  • docking
  • enzyme inhibitor
  • molecular modeling
  • protein–protein interaction
  • structural genomics
  • interactome
  • virtual screening
  • nonstructural proteins
  • spike protein
  • virus–host interaction

Published Papers (2 papers)

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Research

15 pages, 8039 KiB  
Article
Identification of Novel Potential Heparanase Inhibitors Using Virtual Screening
by Alfredo Rus, Victor M. Bolanos-Garcia, Agatha Bastida and Paula Morales
Catalysts 2022, 12(5), 503; https://doi.org/10.3390/catal12050503 - 30 Apr 2022
Cited by 3 | Viewed by 2046
Abstract
Heparanase (HPSE) is a mammalian endo-β-D-glucuronidase that cleaves heparan sulphate (HS) side chains of heparin sulphate proteoglycans (HSPG), a class of molecules composed of repeating polysulfated disaccharide units of glucosamine and hexuronic acid residues. HPSE controls the availability of growth factors, chemokines, lipoproteins [...] Read more.
Heparanase (HPSE) is a mammalian endo-β-D-glucuronidase that cleaves heparan sulphate (HS) side chains of heparin sulphate proteoglycans (HSPG), a class of molecules composed of repeating polysulfated disaccharide units of glucosamine and hexuronic acid residues. HPSE controls the availability of growth factors, chemokines, lipoproteins and other bioactive molecules by degrading HS into smaller fractions, allowing the release of saccharide fragments that activate a plethora of signaling processes. HPSE overexpression has been correlated with tumor survival and metastasis as well as several diseases associated with chronic inflammation, including the ongoing COVID-19 pandemic caused by SARS-CoV-2. Thus, the search for molecules that could potentially inhibit HPSE has become increasingly relevant in the clinic. In this study, we have integrated a strategy that combines virtual screening and molecular docking of publicly available chemical databases to identify small compounds that can be developed into novel HPSE inhibitors. Structural rationalization of the interactions previously reported compounds led us to identify promising unexplored chemotypes. Here we show that these novel potential HPSE inhibitors present optimized in silico druggability and docking properties and may serve as pharmacological tools for the treatment of chronic and infectious diseases associated with chronic inflammation. Full article
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13 pages, 5657 KiB  
Article
Interfering with mRNA Methylation by the 2′O-Methyltransferase (NSP16) from SARS-CoV-2 to Tackle the COVID-19 Disease
by Paula Morales, Natalie L. Curtis, Sandra G. Zárate, Agatha Bastida and Victor M. Bolanos-Garcia
Catalysts 2020, 10(9), 1023; https://doi.org/10.3390/catal10091023 - 05 Sep 2020
Cited by 10 | Viewed by 5741
Abstract
The pandemic associated to Severe Acute Respiratory Syndrome Coronavirus type 2 (SARS-CoV-2) has resulted in a huge number of deaths and infected people. Although several vaccine programmes are currently underway and have reached phase 3, and a few small size drugs repurposed to [...] Read more.
The pandemic associated to Severe Acute Respiratory Syndrome Coronavirus type 2 (SARS-CoV-2) has resulted in a huge number of deaths and infected people. Although several vaccine programmes are currently underway and have reached phase 3, and a few small size drugs repurposed to aid treatment of severe cases of COVID-19 infections, effective therapeutic options for this disease do not currently exist. NSP16 is a S-adenosyl-L-Methionine (SAM) dependent 2′O-Methyltransferase that converts mRNA cap-0 into cap-1 structure to prevent virus detection by cell innate immunity mechanisms. NSP16 methylates the ribose 2′O-position of the first nucleotide of the mRNA only in the presence of an interacting partner, the protein NSP10. This feature suggests that inhibition of the NSP16 may represent a therapeutic window to treat COVID-19. To test this idea, we performed comparative structural analyses of the NSP16 present in human coronaviruses and developed a sinefungin (SFG) similarity-based virtual screening campaign to assess the druggability of the SARS-CoV-2 NSP16 enzyme. Through these studies, we identified the SFG analogue 44601604 as a promising more potent inhibitor of NSP16 to limit viral replication in infected cells, favouring viral clearance. Full article
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