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Cells
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Computational Modeling on Immune Cells in Infectious Diseases
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Computational Modeling on Immune Cells in Infectious Diseases

A special issue of Cells (ISSN 2073-4409). This special issue belongs to the section "Cellular Immunology".

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 15824

Special Issue Editors

Prof. Dr. Francesco Pappalardo

E-Mail Website
Guest Editor
Department of Drug Sciences, University of Catania, 95125 Catania, Italy
Interests: computational immunology; agent-based models; in silico trials; regulatory affairs; systems biomedicine
Special Issues, Collections and Topics in MDPI journals
Dr. Giulia Russo

E-Mail Website
Guest Editor
Department of Drug Sciences, Università degli Studi di Catania, Catania, Italy
Interests: computational immunology; agent-based models; in silico trials; regulatory affairs; kinetic modeling of biological systems

Special Issue Information

Dear Colleagues,

All multicellular organisms have evolved defense mechanisms against the onslaught of pathogens such as viruses, bacteria, and parasites. The immune system of vertebrates combines evolutionarily innate (or natural) immunity, which occurs at the first stage of the infection, with newer adaptive responses against specific pathogens’ antigens. The two systems are tightly integrated, in a network involving a large number of cell types and several molecules. A big challenge is to translate the huge complexity of the immune system into a computational domain.

Through more than fifteen years, several in silico trials infrastructures have been applied to simulate the main features and dynamics of the immune system in several infectious diseases scenarios.

They simulate, to a different extent, both cellular and molecular entities playing a role in the immune system, inside the host and its interactions with the immune system, and the different outcomes originating from a specific disease (e.g., Mycobacterium tuberculosis, influenza virus, SARS-CoV-2). This Special Issue intends to collect contributions from mathematicians, bioinformaticians, computational scientists, and engineers together with experimental immunologists and biologists, to present and discuss the latest developments in different sub-areas ranging from modeling and simulation to in silico predictions, and their application to basic and applied immunology in infectious disease.

Prof. Francesco Pappalardo
Dr. Giulia Russo
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. Cells 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

  • Computational modeling 
  • Immune system dynamics 
  • Infectious diseases 
  • Agent-based models 
  • In silico trials

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Published Papers (3 papers)

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Research

25 pages, 7233 KiB  
Article
In Silico Designing of a Multitope Vaccine against Rhizopus microsporus with Potential Activity against Other Mucormycosis Causing Fungi
by Mohamed A. Soltan, Muhammad Alaa Eldeen, Nada Elbassiouny, Hasnaa L. Kamel, Kareem M. Abdelraheem, Hanaa Abd El-Gayyed, Ahmed M. Gouda, Mohammed F. Sheha, Eman Fayad, Ola A. Abu Ali, Khalid Abd El Ghany, Dalia A. El-damasy, Khaled M. Darwish, Sameh S. Elhady and Ashraf E. Sileem
Cells 2021, 10(11), 3014; https://doi.org/10.3390/cells10113014 - 4 Nov 2021
Cited by 25 | Viewed by 3963
Abstract
During the current era of the COVID-19 pandemic, the dissemination of Mucorales has been reported globally, with elevated rates of infection in India, and because of the high rate of mortality and morbidity, designing an effective vaccine against mucormycosis is a major health [...] Read more.
During the current era of the COVID-19 pandemic, the dissemination of Mucorales has been reported globally, with elevated rates of infection in India, and because of the high rate of mortality and morbidity, designing an effective vaccine against mucormycosis is a major health priority, especially for immunocompromised patients. In the current study, we studied shared Mucorales proteins, which have been reported as virulence factors, and after analysis of several virulent proteins for their antigenicity and subcellular localization, we selected spore coat (CotH) and serine protease (SP) proteins as the targets of epitope mapping. The current study proposes a vaccine constructed based on top-ranking cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL), and B cell lymphocyte (BCL) epitopes from filtered proteins. In addition to the selected epitopes, β-defensins adjuvant and PADRE peptide were included in the constructed vaccine to improve the stimulated immune response. Computational tools were used to estimate the physicochemical and immunological features of the proposed vaccine and validate its binding with TLR-2, where the output data of these assessments potentiate the probability of the constructed vaccine to stimulate a specific immune response against mucormycosis. Here, we demonstrate the approach of potential vaccine construction and assessment through computational tools, and to the best of our knowledge, this is the first study of a proposed vaccine against mucormycosis based on the immunoinformatics approach. Full article
(This article belongs to the Special Issue Computational Modeling on Immune Cells in Infectious Diseases)
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13 pages, 2042 KiB  
Article
CytokineLink: A Cytokine Communication Map to Analyse Immune Responses—Case Studies in Inflammatory Bowel Disease and COVID-19
by Marton Olbei, John P. Thomas, Isabelle Hautefort, Agatha Treveil, Balazs Bohar, Matthew Madgwick, Lejla Gul, Luca Csabai, Dezso Modos and Tamas Korcsmaros
Cells 2021, 10(9), 2242; https://doi.org/10.3390/cells10092242 - 29 Aug 2021
Cited by 6 | Viewed by 5421
Abstract
Intercellular communication mediated by cytokines is critical to the development of immune responses, particularly in the context of infectious and inflammatory diseases. By releasing these small molecular weight peptides, the source cells can influence numerous intracellular processes in the target cells, including the [...] Read more.
Intercellular communication mediated by cytokines is critical to the development of immune responses, particularly in the context of infectious and inflammatory diseases. By releasing these small molecular weight peptides, the source cells can influence numerous intracellular processes in the target cells, including the secretion of other cytokines downstream. However, there are no readily available bioinformatic resources that can model cytokine–cytokine interactions. In this effort, we built a communication map between major tissues and blood cells that reveals how cytokine-mediated intercellular networks form during homeostatic conditions. We collated the most prevalent cytokines from the literature and assigned the proteins and their corresponding receptors to source tissue and blood cell types based on enriched consensus RNA-Seq data from the Human Protein Atlas database. To assign more confidence to the interactions, we integrated the literature information on cell–cytokine interactions from two systems of immunology databases, immuneXpresso and ImmunoGlobe. From the collated information, we defined two metanetworks: a cell–cell communication network connected by cytokines; and a cytokine–cytokine interaction network depicting the potential ways in which cytokines can affect the activity of each other. Using expression data from disease states, we then applied this resource to reveal perturbations in cytokine-mediated intercellular signalling in inflammatory and infectious diseases (ulcerative colitis and COVID-19, respectively). For ulcerative colitis, with CytokineLink, we demonstrated a significant rewiring of cytokine-mediated intercellular communication between non-inflamed and inflamed colonic tissues. For COVID-19, we were able to identify cell types and cytokine interactions following SARS-CoV-2 infection, highlighting important cytokine interactions that might contribute to severe illness in a subgroup of patients. Such findings have the potential to inform the development of novel, cytokine-targeted therapeutic strategies. CytokineLink is freely available for the scientific community through the NDEx platform and the project github repository. Full article
(This article belongs to the Special Issue Computational Modeling on Immune Cells in Infectious Diseases)
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16 pages, 4160 KiB  
Article
Remdesivir and Ledipasvir among the FDA-Approved Antiviral Drugs Have Potential to Inhibit SARS-CoV-2 Replication
by Rameez Hassan Pirzada, Muhammad Haseeb, Maria Batool, MoonSuk Kim and Sangdun Choi
Cells 2021, 10(5), 1052; https://doi.org/10.3390/cells10051052 - 29 Apr 2021
Cited by 29 | Viewed by 5262
Abstract
The rapid spread of the virus, the surge in the number of deaths, and the unavailability of specific SARS-CoV-2 drugs thus far necessitate the identification of drugs with anti-COVID-19 activity. SARS-CoV-2 enters the host cell and assembles a multisubunit RNA-dependent RNA polymerase (RdRp) [...] Read more.
The rapid spread of the virus, the surge in the number of deaths, and the unavailability of specific SARS-CoV-2 drugs thus far necessitate the identification of drugs with anti-COVID-19 activity. SARS-CoV-2 enters the host cell and assembles a multisubunit RNA-dependent RNA polymerase (RdRp) complex of viral nonstructural proteins that plays a substantial role in the transcription and replication of the viral genome. Therefore, RdRp is among the most suitable targets in RNA viruses. Our aim was to investigate the FDA approved antiviral drugs having potential to inhibit the viral replication. The methodology adopted was virtual screening and docking of FDA-approved antiviral drugs into the RdRp protein. Top hits were selected and subjected to molecular dynamics simulations to understand the dynamics of RdRp in complex with these drugs. The antiviral activity of the drugs against SARS-CoV-2 was assessed in Vero E6 cells. Notably, both remdesivir (half-maximal effective concentration (EC50) 6.6 μM, 50% cytotoxicity concentration (CC50) > 100 µM, selectivity index (SI) = 15) and ledipasvir (EC50 34.6 μM, CC50 > 100 µM, SI > 2.9) exerted antiviral action. This study highlights the use of direct-acting antiviral drugs, alone or in combination, for better treatments of COVID-19. Full article
(This article belongs to the Special Issue Computational Modeling on Immune Cells in Infectious Diseases)
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