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Genetic and Structural Analyses of Coronaviruses: Insights into SARS-CoV-2 and...
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Genetic and Structural Analyses of Coronaviruses: Insights into SARS-CoV-2 and Beyond

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Molecular Biophysics: Structure, Dynamics, and Function".

Deadline for manuscript submissions: 30 May 2025 | Viewed by 4335

Special Issue Editor

Prof. Dr. Stefano Pascarella

E-Mail Website
Guest Editor
Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, Piazzale Aldo Moro, 5, 00185 Roma, Italy
Interests: structural bioinformatics; structural biology; protein evolution; protein variants; protein structure and function; protein structure prediction; protein–protein interaction; protein–ligand interaction; genome biology and evolution
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Coronaviruses are a large group of pathogenic viruses circulating in mammals and avians. Epidemic outbreaks have been recurrently caused by coronaviruses, the most recent of which was COVID-19, whose etiologic agent is SARS-CoV-2. 

The relevance of coronaviruses to human health, for example, of SARS-CoV-2, requires rigorous genomic surveillance and studies to understand their molecular complexity and characterize their evolving variants. The findings have immediate implications for human health and therapeutic strategies and, more broadly, may have significance for studies on the molecular evolution of other human viruses. 

We invite researchers to contribute to a Special Issue that delves into the molecular genetics and structural analyses of coronaviruses and their proteins using theoretical and/or experimental approaches. This Special Issue aims to bring together cutting-edge and high-quality research that elucidates the molecular basis of these viruses, their transmission dynamics, and implications for human health and treatments. Topics of interest can be summarized, not exclusively, as follows: 

  • The genomic characterization of coronaviruses and variants.
  • Structural analyses of variant viral proteins and their functional implications also serving as targets for drugs.
  • Evolutionary dynamics and mutation hotspots.
  • Molecular host–virus interactions, pathogenesis, and immune responses.
  • Implications for molecular diagnostics, therapeutics, and vaccine development.

Prof. Dr. Stefano Pascarella
Guest Editor

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. Biomolecules is an international peer-reviewed open access monthly 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 variants
  • protein variants
  • protein structure
  • virus evolution
  • mutations
  • structural bioinformatics
  • molecular phylogenesis
  • host–pathogen molecular interactions
  • molecular immunology
  • drug discovery

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Published Papers (4 papers)

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Research

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32 pages, 8910 KiB  
Article
Subtle Changes at the RBD/hACE2 Interface During SARS-CoV-2 Variant Evolution: A Molecular Dynamics Study
by Aria Gheeraert, Vincent Leroux, Dominique Mias-Lucquin, Yasaman Karami, Laurent Vuillon, Isaure Chauvot de Beauchêne, Marie-Dominique Devignes, Ivan Rivalta, Bernard Maigret and Laurent Chaloin
Biomolecules 2025, 15(4), 541; https://doi.org/10.3390/biom15040541 - 7 Apr 2025
Viewed by 427
Abstract
The SARS-CoV-2 Omicron variants show different behavior compared to the previous variants, especially with respect to the Delta variant, which promotes a lower morbidity despite being much more contagious. In this perspective, we performed molecular dynamics (MD) simulations of the different spike RBD/hACE2 [...] Read more.
The SARS-CoV-2 Omicron variants show different behavior compared to the previous variants, especially with respect to the Delta variant, which promotes a lower morbidity despite being much more contagious. In this perspective, we performed molecular dynamics (MD) simulations of the different spike RBD/hACE2 complexes corresponding to the WT, Delta and four Omicron variants. Carrying out a comprehensive analysis of residue interactions within and between the two partners allowed us to draw the profile of each variant by using complementary methods (PairInt, hydrophobic potential, contact PCA). PairInt calculations highlighted the residues most involved in electrostatic interactions, which make a strong contribution to the binding with highly stable interactions between spike RBD and hACE2. Apolar contacts made a substantial and complementary contribution in Omicron with the detection of two hydrophobic patches. Contact networks and cross-correlation matrices were able to detect subtle changes at point mutations as the S375F mutation occurring in all Omicron variants, which is likely to confer an advantage in binding stability. This study brings new highlights on the dynamic binding of spike RBD to hACE2, which may explain the final persistence of Omicron over Delta. Full article
(This article belongs to the Special Issue Genetic and Structural Analyses of Coronaviruses: Insights into SARS-CoV-2 and Beyond)
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36 pages, 6863 KiB  
Article
Quantitative Characterization and Prediction of the Binding Determinants and Immune Escape Hotspots for Groups of Broadly Neutralizing Antibodies Against Omicron Variants: Atomistic Modeling of the SARS-CoV-2 Spike Complexes with Antibodies
by Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Nishank Raisinghani and Gennady Verkhivker
Biomolecules 2025, 15(2), 249; https://doi.org/10.3390/biom15020249 - 8 Feb 2025
Viewed by 781
Abstract
A growing body of experimental and computational studies suggests that the cross-neutralization antibody activity against Omicron variants may be driven by the balance and tradeoff between multiple energetic factors and interaction contributions of the evolving escape hotspots involved in antigenic drift and convergent [...] Read more.
A growing body of experimental and computational studies suggests that the cross-neutralization antibody activity against Omicron variants may be driven by the balance and tradeoff between multiple energetic factors and interaction contributions of the evolving escape hotspots involved in antigenic drift and convergent evolution. However, the dynamic and energetic details quantifying the balance and contribution of these factors, particularly the balancing nature of specific interactions formed by antibodies with epitope residues, remain largely uncharacterized. In this study, we performed molecular dynamics simulations, an ensemble-based deep mutational scanning of SARS-CoV-2 spike residues, and binding free energy computations for two distinct groups of broadly neutralizing antibodies: the E1 group (BD55-3152, BD55-3546, and BD5-5840) and the F3 group (BD55-3372, BD55-4637, and BD55-5514). Using these approaches, we examined the energetic determinants by which broadly potent antibodies can largely evade immune resistance. Our analysis revealed the emergence of a small number of immune escape positions for E1 group antibodies that correspond to the R346 and K444 positions in which the strong van der Waals and interactions act synchronously, leading to the large binding contribution. According to our results, the E1 and F3 groups of Abs effectively exploit binding hotspot clusters of hydrophobic sites that are critical for spike functions along with the selective complementary targeting of positively charged sites that are important for ACE2 binding. Together with targeting conserved epitopes, these groups of antibodies can lead expand the breadth and resilience of neutralization to the antigenic shifts associated with viral evolution. The results of this study and the energetic analysis demonstrate excellent qualitative agreement between the predicted binding hotspots and critical mutations with respect to the latest experiments on average antibody escape scores. We argue that the E1 and F3 groups of antibodies targeting binding epitopes may leverage strong hydrophobic interactions with the binding epitope hotspots that are critical for the spike stability and ACE2 binding, while escape mutations tend to emerge in sites associated with synergistically strong hydrophobic and electrostatic interactions. Full article
(This article belongs to the Special Issue Genetic and Structural Analyses of Coronaviruses: Insights into SARS-CoV-2 and Beyond)
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20 pages, 4992 KiB  
Article
Membrane Activity and Viroporin Assembly for the SARS-CoV-2 E Protein Are Regulated by Cholesterol
by Marta V. Volovik, Zaret G. Denieva, Polina K. Gifer, Maria A. Rakitina and Oleg V. Batishchev
Biomolecules 2024, 14(9), 1061; https://doi.org/10.3390/biom14091061 - 26 Aug 2024
Cited by 2 | Viewed by 1441
Abstract
The SARS-CoV-2 E protein is an enigmatic viral structural protein with reported viroporin activity associated with the acute respiratory symptoms of COVID-19, as well as the ability to deform cell membranes for viral budding. Like many viroporins, the E protein is thought to [...] Read more.
The SARS-CoV-2 E protein is an enigmatic viral structural protein with reported viroporin activity associated with the acute respiratory symptoms of COVID-19, as well as the ability to deform cell membranes for viral budding. Like many viroporins, the E protein is thought to oligomerize with a well-defined stoichiometry. However, attempts to determine the structure of the protein complex have yielded inconclusive results, suggesting several possible oligomers, ranging from dimers to pentamers. Here, we combined patch-clamp, confocal fluorescence microscopy on giant unilamellar vesicles, and atomic force microscopy to show that E protein can exhibit two modes of membrane activity depending on membrane lipid composition. In the absence or the presence of a low content of cholesterol, the protein forms short-living transient pores, which are seen as semi-transmembrane defects in a membrane by atomic force microscopy. Approximately 30 mol% cholesterol is a threshold for the transition to the second mode of conductance, which could be a stable pentameric channel penetrating the entire lipid bilayer. Therefore, the E-protein has at least two different types of activity on membrane permeabilization, which are regulated by the amount of cholesterol in the membrane lipid composition and could be associated with different types of protein oligomers. Full article
(This article belongs to the Special Issue Genetic and Structural Analyses of Coronaviruses: Insights into SARS-CoV-2 and Beyond)
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Review

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19 pages, 1906 KiB  
Review
Sequences in the Cytoplasmic Tail Contribute to the Intracellular Trafficking and the Cell Surface Localization of SARS-CoV-2 Spike Protein
by Evgeniya E. Burkova and Irina A. Bakhno
Biomolecules 2025, 15(2), 280; https://doi.org/10.3390/biom15020280 - 14 Feb 2025
Viewed by 1085
Abstract
Spike protein is a surface glycoprotein of the SARS-CoV-2 coronavirus, providing interaction of the coronavirus with angiotensin-converting enzyme 2 (ACE2) on the host cell. The cytoplasmic tail of the S protein plays an important role in an intracellular transport and translocation of the [...] Read more.
Spike protein is a surface glycoprotein of the SARS-CoV-2 coronavirus, providing interaction of the coronavirus with angiotensin-converting enzyme 2 (ACE2) on the host cell. The cytoplasmic tail of the S protein plays an important role in an intracellular transport and translocation of the glycoprotein to the plasma membrane. The cytoplasmic domain of the S protein contains binding sites for COPI, COPII, and SNX27, which are required for the intracellular trafficking of this glycoprotein. In addition, the cytoplasmic domain of the S protein contains S-palmitoylation sites. S-palmitoylation increases the hydrophobicity of the S protein by regulating its transport to the plasma membrane. The cytoplasmic tail of the S protein has a signaling sequence that provides interaction with the ERM family proteins, which may mediate communication between the cell membrane and the actin cytoskeleton. This review examines the role of the cytoplasmic tail of the SARS-CoV-2 S protein in its intracellular transport and translocation to the plasma membrane. Understanding these processes is necessary not only for the development of vaccines based on mRNA or adenovirus vectors encoding the full-length spike (S) protein, but also for the therapy of the new coronavirus infection (COVID-19). Full article
(This article belongs to the Special Issue Genetic and Structural Analyses of Coronaviruses: Insights into SARS-CoV-2 and Beyond)
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