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Biomolecules
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Molecular Mechanisms of Infectious Pathogen Adaptation, Emergence, and Re-emergence
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Molecular Mechanisms of Infectious Pathogen Adaptation, Emergence, and Re-emergence

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Molecular Medicine".

Deadline for manuscript submissions: closed (31 May 2025) | Viewed by 8369

Special Issue Editors

Dr. Rita Berisio

E-Mail Website
Guest Editor
Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
Interests: structural biology; biophysics; infectious diseases; vaccine
Special Issues, Collections and Topics in MDPI journals
Dr. Alessia Ruggiero

E-Mail Website
Guest Editor
Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
Interests: structural biology; molecular biology; biochemistry; infection disease
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Pathogen emergence is a complex phenomenon due to multiple factors, like genetic adaptations, selective pressure by the human host, and antibiotic or antiviral pressure. Among re-emerging respiratory pathogens, tuberculosis (TB) is one of the leading causes of death by infection, especially in immunocompromised patients (e.g., those with HIV). Rising rates of TB antibiotic resistance have been recorded around the world, making these bacteria immune to anti-TB drugs. TB can persist in many infected individuals in a latent state for many years and can be reactivated to cause disease. Children and adults with other disease like HIV are more prone to being affected. In most healthy people, the immune system can destroy the bacteria, whereas in some cases, TB infection begins without symptoms before becoming active (latent TB) and can persist for weeks, months, or years. New antibacterial strategies are needed to manage the global challenge of antimicrobial resistance in TB infection, to tackle both active TB and the threat of M. tuberculosis resuscitation. Also, the ESKAPE group of pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, A. baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) are leading causes of nosocomial infections, with some of them declared by the World Health Organization (WHO) as critical, owing to their formidable adaptability and resistance to antimicrobial therapies. Adaptation mechanisms to drugs and to the host are also the ace in the hole of pandemic viruses, like SARS-CoV2, which exploit the host to enhance their viral infecting efficacy.

To address all these issues, comprehensive knowledge of important macromolecules regulating pathogen physiopathology is essential. In the last few decades, extensive studies have been performed aimed at the structural and functional characterization of the key molecular players involved virulence and adaptation to either drugs or to their hosts. This Special Issue offers an open access platform that aims to bring together a collection of research articles, reviews, and perspectives to address various aspects of pathogen emergence and re-emergence and the development of therapeutic tools against difficult pathogens.

Dr. Rita Berisio
Dr. Alessia Ruggiero
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. 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

  • pathogen
  • structural biology
  • tuberculosis
  • function
  • molecular mechanism

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Related Special Issue

Published Papers (5 papers)

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Research

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16 pages, 2249 KiB  
Article
Elucidating the Role of Toxoplama gondii’s Mitochondrial Superoxide Dismutase
by James Alexander Tirtorahardjo, Christopher I-H. Ma, Areej Shaikh and Rosa M. Andrade
Biomolecules 2025, 15(7), 972; https://doi.org/10.3390/biom15070972 - 7 Jul 2025
Viewed by 78
Abstract
Toxoplasma gondii is an Apicomplexan parasite that possesses a well-developed system of scavengers of reactive oxygen species (ROS). Among its components, T. gondii mitochondrial superoxide dismutase (TgSOD2) is essential, as predicted by the CRISPR phenotype index and evidenced by the non-viability of its [...] Read more.
Toxoplasma gondii is an Apicomplexan parasite that possesses a well-developed system of scavengers of reactive oxygen species (ROS). Among its components, T. gondii mitochondrial superoxide dismutase (TgSOD2) is essential, as predicted by the CRISPR phenotype index and evidenced by the non-viability of its constitutive knockouts. As an obligate intracellular parasite, TgSOD2 is upregulated during extracellular stages. Herein, we generated a viable TgSOD2 knockdown mutant using an inducible auxin–degron system to explore the biological role of TgSOD2 in T. gondii. Depletion of TgSOD2 led to impaired parasite growth and replication, reduced mitochondrial membrane potential (MMP), abnormalities in the distribution of ATP synthase within its mitochondrial electron transport chain (mETC), and increased susceptibility to mETC inhibitors. Through a proximal biotinylation approach, we identified the interactions of TgSOD2 with complexes IV and V of its mETC, suggesting that these sites are sensitive to ROS. Our study provides the first insights into the role of TgSOD2 in maintaining its mitochondrial redox homeostasis and subsequent parasite replication fitness. Significance: Toxoplasma gondii infects nearly a third of the world population and can cause fetal miscarriages or life-threatening complications in vulnerable patients. Current therapies do not eradicate the parasite from the human hosts, rendering them at risk of recurrence during their lifetimes. T. gondii has a single mitochondrion, which is well-known for its susceptibility to oxidative damage that leads to T. gondii’s death. Therefore, targeting T. gondii mitochondrion remains an attractive therapeutic strategy for drug development. T. gondii’s mitochondrial superoxide dismutase is an antioxidant protein in the parasite mitochondrion and is essential for its survival. Understanding its biological role could reveal mitochondrial vulnerabilities in T. gondii and provide new leads for the development of effective treatments for T. gondii infections. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Infectious Pathogen Adaptation, Emergence, and Re-emergence)
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14 pages, 5362 KiB  
Article
Intratracheal Aerosolization of Nocardia farcinica in Mice Optimizes Bacterial Distribution and Enhances Pathogenicity Compared to Intranasal Inoculation and Intratracheal Instillation
by Bingqian Du, Ziyu Song, Jirao Shen, Jiang Yao, Shuai Xu, Xiaotong Qiu, Min Yuan and Zhenjun Li
Biomolecules 2025, 15(7), 950; https://doi.org/10.3390/biom15070950 - 30 Jun 2025
Viewed by 160
Abstract
Nocardia, an easily missed but potentially fatal opportunistic pathogen, can lead to serious infections like lung and brain abscesses. Intranasal inoculation (IN) is the traditional approach for constructing a Nocardia-induced pneumonia mice model, while it usually only results in limited local [...] Read more.
Nocardia, an easily missed but potentially fatal opportunistic pathogen, can lead to serious infections like lung and brain abscesses. Intranasal inoculation (IN) is the traditional approach for constructing a Nocardia-induced pneumonia mice model, while it usually only results in limited local bacterial infection in the lungs. To comprehensively assess infection dynamics across distinct pulmonary inoculation routes in mice models, this study compared the pathogenicity of three different Nocardia farcinica pneumonia models established via IN, intratracheal aerosolization (ITA), and intratracheal instillation (ITI). C57BL/6J mice were infected with N. farcinica through IN, ITA and ITI with comparative analyses of bacterial distribution in lungs, survival rate, weight, bacterial load, inflammatory cytokines, histopathological characteristics and transcriptome differences. The findings suggest that ITA N. farcinica infections caused severer clinical symptoms, higher mortality, pulmonary bacterial load, levels of inflammatory cytokines in bronchoalveolar lavage fluid, and more significant histopathological damage to lungs than IN and ITI. Furthermore, ITA resulted in better lung bacterial distribution and delivery efficiency than ITI and IN. Transcriptome analysis of lungs from N. farcinica infected mice via IN, ITA and ITI revealed significant differential gene expression, whereas ITA route resulted in a larger fold change. ITA provides a more consistent and severe model of N. farcinica pneumonia in mice than IN and ITI, which can make the bacteria more evenly distributed in the lungs, leading to more severe pathological damage and higher mortality rates. In conclusion, ITA is an optimal route for developing animal models of N. farcinica pneumonia infections. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Infectious Pathogen Adaptation, Emergence, and Re-emergence)
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23 pages, 4569 KiB  
Article
Epimaps of the SARS-CoV-2 Receptor-Binding Domain Mutational Landscape: Insights into Protein Stability, Epitope Prediction, and Antibody Binding
by Eleni Pitsillou, Assam El-Osta, Andrew Hung and Tom C. Karagiannis
Biomolecules 2025, 15(2), 301; https://doi.org/10.3390/biom15020301 - 18 Feb 2025
Cited by 1 | Viewed by 1212
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants poses an ongoing threat to the efficacy of vaccines and therapeutic antibodies. Mutations predominantly affect the receptor-binding domain (RBD) of the spike protein, which mediates viral entry. The RBD is also a [...] Read more.
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants poses an ongoing threat to the efficacy of vaccines and therapeutic antibodies. Mutations predominantly affect the receptor-binding domain (RBD) of the spike protein, which mediates viral entry. The RBD is also a major target of monoclonal antibodies that were authorised for use during the pandemic. In this study, an in silico approach was used to investigate the mutational landscape of SARS-CoV-2 RBD variants, including currently circulating Omicron subvariants. A total of 40 single-point mutations were assessed for their potential effect on protein stability and dynamics. Destabilising effects were predicted for mutations such as L455S and F456L, while stabilising effects were predicted for mutations such as R346T. Conformational B-cell epitope predictions were subsequently performed for wild-type (WT) and variant RBDs. Mutations from SARS-CoV-2 variants were located within the predicted epitope residues and the epitope regions were found to correspond to the sites targeted by therapeutic antibodies. Furthermore, homology models of the RBD of SARS-CoV-2 variants were generated and were utilised for protein–antibody docking. The binding characteristics of 10 monoclonal antibodies against WT and 14 SARS-CoV-2 variants were evaluated. Through evaluating the binding affinities, interactions, and energy contributions of RBD residues, mutations that were contributing to viral evasion were identified. The findings from this study provide insight into the structural and molecular mechanisms underlying neutralising antibody evasion. Future antibody development could focus on broadly neutralising antibodies, engineering antibodies with enhanced binding affinity, and targeting spike protein regions beyond the RBD. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Infectious Pathogen Adaptation, Emergence, and Re-emergence)
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Review

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11 pages, 4772 KiB  
Review
HtpG—A Major Virulence Factor and a Promising Vaccine Antigen against Mycobacterium tuberculosis
by Rita Berisio, Giovanni Barra, Valeria Napolitano, Mario Privitera, Maria Romano, Flavia Squeglia and Alessia Ruggiero
Biomolecules 2024, 14(4), 471; https://doi.org/10.3390/biom14040471 - 11 Apr 2024
Cited by 1 | Viewed by 2257
Abstract
Tuberculosis (TB) is the leading global cause of death f rom an infectious bacterial agent. Therefore, limiting its epidemic spread is a pressing global health priority. The chaperone-like protein HtpG of M. tuberculosis (Mtb) is a large dimeric and multi-domain protein with a [...] Read more.
Tuberculosis (TB) is the leading global cause of death f rom an infectious bacterial agent. Therefore, limiting its epidemic spread is a pressing global health priority. The chaperone-like protein HtpG of M. tuberculosis (Mtb) is a large dimeric and multi-domain protein with a key role in Mtb pathogenesis and promising antigenic properties. This dual role, likely associated with the ability of Heat Shock proteins to act both intra- and extra-cellularly, makes HtpG highly exploitable both for drug and vaccine development. This review aims to gather the latest updates in HtpG structure and biological function, with HtpG operating in conjunction with a large number of chaperone molecules of Mtb. Altogether, these molecules help Mtb recovery after exposure to host-like stress by assisting the whole path of protein folding rescue, from the solubilisation of aggregated proteins to their refolding. Also, we highlight the role of structural biology in the development of safer and more effective subunit antigens. The larger availability of structural information on Mtb antigens and a better understanding of the host immune response to TB infection will aid the acceleration of TB vaccine development. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Infectious Pathogen Adaptation, Emergence, and Re-emergence)
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18 pages, 1057 KiB  
Review
An Overview of SARS-CoV-2 Etiopathogenesis and Recent Developments in COVID-19 Vaccines
by Dona Susan Mathew, Tirtha Pandya, Het Pandya, Yuzen Vaghela and Selvakumar Subbian
Biomolecules 2023, 13(11), 1565; https://doi.org/10.3390/biom13111565 - 24 Oct 2023
Cited by 4 | Viewed by 3576
Abstract
The Coronavirus disease-2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has significantly impacted the health and socioeconomic status of humans worldwide. Pulmonary infection of SARS-CoV-2 results in exorbitant viral replication and associated onset of inflammatory cytokine storm and disease pathology [...] Read more.
The Coronavirus disease-2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has significantly impacted the health and socioeconomic status of humans worldwide. Pulmonary infection of SARS-CoV-2 results in exorbitant viral replication and associated onset of inflammatory cytokine storm and disease pathology in various internal organs. However, the etiopathogenesis of SARS-CoV-2 infection is not fully understood. Currently, there are no targeted therapies available to cure COVID-19, and most patients are treated empirically with anti-inflammatory and/or anti-viral drugs, based on the disease symptoms. Although several types of vaccines are currently implemented to control COVID-19 and prevent viral dissemination, the emergence of new variants of SARS-CoV-2 that can evade the vaccine-induced protective immunity poses challenges to current vaccination strategies and highlights the necessity to develop better and improved vaccines. In this review, we summarize the etiopathogenesis of SARS-CoV-2 and elaborately discuss various types of vaccines and vaccination strategies, focusing on those vaccines that are currently in use worldwide to combat COVID-19 or in various stages of clinical development to use in humans. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Infectious Pathogen Adaptation, Emergence, and Re-emergence)
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