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Biochemistry and Molecular Biology of Coronaviruses
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Biochemistry and Molecular Biology of Coronaviruses

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: 20 December 2025 | Viewed by 3906

Special Issue Editor

Dr. Shu-Qun Liu

E-Mail Website
Guest Editor
1. Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, China
2. Key Laboratory for Tumor Molecular Biology of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming 650091, China
Interests: QSAR

Special Issue Information

Dear Colleagues,

This Special Issue focuses on the biochemistry and molecular biology of coronaviruses, which are RNA viruses responsible for global health crises like SARS-CoV, MERS-CoV, and SARS-CoV-2 (the cause of COVID-19).   Understanding their molecular mechanisms is essential for developing effective therapies and preventive measures.

We invite original research articles and comprehensive reviews exploring aspects such as viral replication, transcription, protein synthesis, assembly and egress pathways, viral protein structure and function, genome organization, host–virus interactions, and drug development. Studies employing advanced techniques such as cryo-electron microscopy, X-ray crystallography, next-generation sequencing, proteomics, computational modeling, and innovative in vitro and in vivo approaches are also highly valued. Topics of interest include host immune responses, immune evasion strategies, the roles of non-structural and accessory proteins in pathogenesis, the emergence of new variants, and the identification of novel antiviral targets. Research focusing on antiviral therapies, including drugs and vaccines, and diagnostic tools grounded in molecular insights is also welcome.

By disseminating cutting-edge research and fostering collaboration among scientists dedicated to unraveling the molecular complexities of coronaviruses, this Special Issue aims to advance our understanding of coronaviruses.   We hope to support global efforts to manage and prevent coronavirus-related health challenges, paving the way for more effective diagnostic tools, therapeutic interventions, and preventive strategies to safeguard global health.

Dr. Shu-Qun Liu
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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
  • MERS-CoV
  • COVID-19
  • RNA viruses
  • infection
  • antivirals
  • vaccines
  • therapeutics
  • host-virus interactions

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Published Papers (3 papers)

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Research

11 pages, 1034 KB  
Communication
The Clinical Significance of GRP78 in COVID-19 Pneumonia Across Two Regional Cohorts
by Steliyan Petrov, Martina Bozhkova, Stanislava Popova-Belova, Mariela Geneva-Popova, Tanya Deneva, İbrahim Türkçüer and Aylin Köseler
Int. J. Mol. Sci. 2025, 26(21), 10312; https://doi.org/10.3390/ijms262110312 - 23 Oct 2025
Viewed by 19
Abstract
COVID-19 pneumonia remains a major driver of morbidity and mortality worldwide, with outcomes influenced by demographic, clinical, and systemic factors. Glucose-regulated protein 78 (GRP78) has emerged as a potential biomarker of disease severity, but its clinical significance across different populations remains underexplored. We [...] Read more.
COVID-19 pneumonia remains a major driver of morbidity and mortality worldwide, with outcomes influenced by demographic, clinical, and systemic factors. Glucose-regulated protein 78 (GRP78) has emerged as a potential biomarker of disease severity, but its clinical significance across different populations remains underexplored. We conducted a retrospective cohort study including 83 hospitalized COVID-19 patients from General Hospital “Sv. Georgi”, Plovdiv, Bulgaria, and 97 from Denizli, Türkiye. Pneumonia diagnosis was based on clinical, laboratory, and radiological criteria. Patient demographics and biomarkers (CRP, D-dimer, oxygen saturation, lymphocyte count, and serum GRP78) were compared between cohorts. Statistical analyses included Mann–Whitney U, t-tests, and logistic regression. Pneumonia prevalence was 48.8% in patients from General Hospital “Sv. Georgi”, Plovdiv and 58.8% in Denizli. Patients in Plovdiv were older and exhibited higher CRP, D-dimer, and GRP78 levels, alongside lower oxygen saturation and lymphocyte counts. Logistic regression demonstrated that GRP78 significantly predicted pneumonia in both cohorts, with robust discriminative performance on ROC analysis. This study highlights significant regional differences in COVID-19 pneumonia presentation between Bulgaria and Türkiye. Elevated GRP78 levels were strongly associated with pneumonia and other severity markers, underscoring its potential as a clinically valuable biomarker for early risk stratification. These findings emphasize the importance of both localized epidemiological analyses and biomarker-based approaches to optimize COVID-19 management. Full article
(This article belongs to the Special Issue Biochemistry and Molecular Biology of Coronaviruses)
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17 pages, 432 KB  
Article
Patterns of Recombination in Coronaviruses
by Ricardo Soares, Cristina P. Vieira and Jorge Vieira
Int. J. Mol. Sci. 2025, 26(12), 5595; https://doi.org/10.3390/ijms26125595 - 11 Jun 2025
Viewed by 818
Abstract
By bringing together different variant combinations, recombination can contribute to adaptation in Coronaviridae species, some of which infect humans, and have given rise to epidemics and a pandemic. Therefore, in this work, the impact of the use of different recombination inference methods and [...] Read more.
By bringing together different variant combinations, recombination can contribute to adaptation in Coronaviridae species, some of which infect humans, and have given rise to epidemics and a pandemic. Therefore, in this work, the impact of the use of different recombination inference methods and sample sizes is addressed using data from 21 Coronaviridae species, and recombination inferences are further supported using a phylogenetic approach. Recombination patterns are shown not to vary greatly between species. A positive correlation is found between gene position and recombination rates, suggesting intrinsic variation in recombination rates along the genome. Within and between species recombination patterns are shown to differ, the module type being the most prevalent between species except for the Membrane and Nucleocapsid genes, whose products are known to interact and thus must co-evolve, explaining why the two genes are often recombined as one unit. It is also shown that within species, the module type is prevalent for the Spike gene only. Moreover, a positive correlation between recombination and selection is here reported. Therefore, intratypic recombination patterns are also shaped by selection. Recombination may thus be an important source of variability upon which selection can act. Full article
(This article belongs to the Special Issue Biochemistry and Molecular Biology of Coronaviruses)
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22 pages, 4648 KB  
Article
Dissecting the Binding Affinity of Anti-SARS-CoV-2 Compounds to Human Transmembrane Protease, Serine 2: A Computational Study
by Yue-Hui Shi, Jian-Xin Shen, Yan Tao, Yuan-Ling Xia, Zhi-Bi Zhang, Yun-Xin Fu, Ke-Qin Zhang and Shu-Qun Liu
Int. J. Mol. Sci. 2025, 26(2), 587; https://doi.org/10.3390/ijms26020587 - 11 Jan 2025
Viewed by 1966
Abstract
The human transmembrane protease, serine 2 (TMPRSS2), essential for SARS-CoV-2 entry, is a key antiviral target. Here, we computationally profiled the TMPRSS2-binding affinities of 15 antiviral compounds. Molecular dynamics (MD) simulations for the docked complexes revealed that three compounds exited the substrate-binding cavity [...] Read more.
The human transmembrane protease, serine 2 (TMPRSS2), essential for SARS-CoV-2 entry, is a key antiviral target. Here, we computationally profiled the TMPRSS2-binding affinities of 15 antiviral compounds. Molecular dynamics (MD) simulations for the docked complexes revealed that three compounds exited the substrate-binding cavity (SBC), suggesting noncompetitive inhibition. Of the remaining compounds, five charged ones exhibited reduced binding stability due to competing electrostatic interactions and increased solvent exposure, while seven neutral compounds showed stronger binding affinity driven by van der Waals (vdW) interactions compensating for unfavorable electrostatic effects (including electrostatic interactions and desolvation penalties). Positive and negative hotspot residues were identified as uncharged and charged, respectively, both lining the SBC. Despite forming diverse interactions with compounds, the burial of positive hotspots led to strong vdW interactions that overcompensated for unfavorable electrostatic effects, whereas negative hotspots incurred high desolvation penalties, negating any favorable contributions. Charged residues at the SBC’s outer rim can reduce binding affinity significantly when forming hydrogen bonds or salt bridges. These findings underscore the importance of enhancing vdW interactions with uncharged residues and minimizing the unfavorable electrostatic effects of charged residues, providing valuable insights for designing effective TMPRSS2 inhibitors. Full article
(This article belongs to the Special Issue Biochemistry and Molecular Biology of Coronaviruses)
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