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Pathogens
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Computational Approaches in Mechanisms of Pathogenesis
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Computational Approaches in Mechanisms of Pathogenesis

A special issue of Pathogens (ISSN 2076-0817). This special issue belongs to the section "Viral Pathogens".

Deadline for manuscript submissions: 10 October 2025 | Viewed by 10983

Special Issue Editor

Dr. Shaneen M. Singh

E-Mail Website
Guest Editor
Department of Biology, Brooklyn College, Brooklyn, NY 11210, USA
Interests: bioinformatics; structural biology; computational biology approaches

Special Issue Information

Dear Colleagues,

Computational biology approaches are becoming popular and are at the forefront of theoretical and experimental biology. They provide a novel way of looking at complex biological problems and provide unique insights that are often unobtainable using other approaches; computational approaches have become an integral part of a biologist’s toolkit in framing new questions, formulating rational experimental designs and aiding the analysis of experimental results. Thus, the development of these tools has influenced and radically evolved all biological sciences. In this special edition of Pathogens, we focus on computational approaches that can lead to obtaining novel insights into pathogenic mechanisms.

I would like to invite colleagues investigating mechanisms of pathogenesis using in silico approaches alone or in combination with experimental findings to submit their manuscripts to this Special Issue in the form of original research and reviews.

Dr. Shaneen M. Singh
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. Pathogens 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 2200 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 biology
  • bioinformatics
  • in silico approaches
  • simulations
  • pathogenesis

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Published Papers (6 papers)

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Research

Jump to: Review

16 pages, 2378 KiB  
Communication
In Silico Targeting and Immunological Profiling of PpiA in Mycobacterium tuberculosis: A Computational Approach
by Mohammad J. Nasiri, Lily Rogowski and Vishwanath Venketaraman
Pathogens 2025, 14(4), 370; https://doi.org/10.3390/pathogens14040370 - 9 Apr 2025
Viewed by 537
Abstract
Tuberculosis (TB) remains a leading cause of mortality, with drug resistance highlighting the need for new vaccine targets. Peptidyl-prolyl isomerase A (PpiA), a conserved Mycobacterium tuberculosis (Mtb) protein, plays a role in bacterial stress adaptation and immune evasion, making it a potential target [...] Read more.
Tuberculosis (TB) remains a leading cause of mortality, with drug resistance highlighting the need for new vaccine targets. Peptidyl-prolyl isomerase A (PpiA), a conserved Mycobacterium tuberculosis (Mtb) protein, plays a role in bacterial stress adaptation and immune evasion, making it a potential target for immunotherapy. This study uses computational methods to assess PpiA’s antigenicity, structural integrity, and immunogenic potential. The PpiA sequence was retrieved from NCBI and analyzed for antigenicity and allergenicity using VaxiJen, AllerTOP, and AllergenFP. Physicochemical properties were evaluated using ProtParam, and structural models were generated through PSIPRED and SWISS-MODEL. Structural validation was performed with MolProbity, QMEANDisCo, and ProSA-Web. B-cell epitopes were predicted using BepiPred 2.0 and IEDB, while T-cell epitopes were mapped via IEDB’s MHC-I and MHC-II tools. Epitope conservation across Mtb strains was confirmed using ConSurf. Results indicate PpiA is highly antigenic, non-allergenic, and stable, with several immunogenic epitopes identified for both B- and T-cells. This study supports PpiA as a promising immunogenic target for TB vaccine development. Full article
(This article belongs to the Special Issue Computational Approaches in Mechanisms of Pathogenesis)
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20 pages, 1300 KiB  
Article
Venomous Cargo: Diverse Toxin-Related Proteins Are Associated with Extracellular Vesicles in Parasitoid Wasp Venom
by Jennifer Chou, Michael Z. Li, Brian Wey, Mubasshir Mumtaz, Johnny R. Ramroop, Shaneen Singh and Shubha Govind
Pathogens 2025, 14(3), 255; https://doi.org/10.3390/pathogens14030255 - 5 Mar 2025
Viewed by 857
Abstract
Unusual membrane-bound particles are present in the venom of the parasitoid wasps that parasitize Drosophila melanogaster. These venom particles harbor about 400 proteins and suppress the encapsulation of a wasp egg. Whereas the proteins in the particles of Leptopilina boulardi venom modify host hemocyte [...] Read more.
Unusual membrane-bound particles are present in the venom of the parasitoid wasps that parasitize Drosophila melanogaster. These venom particles harbor about 400 proteins and suppress the encapsulation of a wasp egg. Whereas the proteins in the particles of Leptopilina boulardi venom modify host hemocyte properties, those in L. heterotoma kill host hemocytes. The mechanisms underlying this differential effect are not well understood. The proteome of the L. heterotoma venom particles has been described before, but that of L. boulardi has not been similarly examined. Using sequence-based programs, we report the presence of conserved proteins in both proteomes with strong enrichment in the endomembrane and exosomal cell components. Extracellular vesicle markers are present in both proteomes, as are numerous toxins. Both proteomes also contain proteins lacking any annotation. Among these, we identified the proteins with structural similarity to the ADP-ribosyltransferase enzymes involved in bacterial virulence. We propose that invertebrate fluids like parasitoid venom contain functional extracellular vesicles that deliver toxins and virulence factors from a parasite to a host. Furthermore, the presence of such vesicles may not be uncommon in the venom of other animals. An experimental verification of the predicted toxin functions will clarify the cellular mechanisms underlying successful parasitism. Full article
(This article belongs to the Special Issue Computational Approaches in Mechanisms of Pathogenesis)
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19 pages, 3153 KiB  
Article
Genome-Wide Approach Identifies Natural Large-Fragment Deletion in ASFV Strains Circulating in Italy During 2023
by Claudia Torresi, Roberta Biccheri, Cesare Cammà, Carmina Gallardo, Maurilia Marcacci, Simona Zoppi, Barbara Secondini, Caterina Riverso, Alejandro Soler, Cristina Casciari, Michela Pela, Elisabetta Rossi, Claudia Pellegrini, Carmen Iscaro, Francesco Feliziani and Monica Giammarioli
Pathogens 2025, 14(1), 51; https://doi.org/10.3390/pathogens14010051 - 10 Jan 2025
Viewed by 966
Abstract
African swine fever (ASF), characterized by high mortality rates in infected animals, remains a significant global veterinary and economic concern, due to the widespread distribution of ASF virus (ASFV) genotype II across five continents. In this study, ASFV strains collected in Italy during [...] Read more.
African swine fever (ASF), characterized by high mortality rates in infected animals, remains a significant global veterinary and economic concern, due to the widespread distribution of ASF virus (ASFV) genotype II across five continents. In this study, ASFV strains collected in Italy during 2022–2023 from two geographical clusters, North-West (Alessandria) and Calabria, were fully sequenced. In addition, an in vivo experiment in pigs was performed. Complete genomic sequencing of 30 strains revealed large-fragment deletions and translocations. In Alessandria, five samples showed two different deletions in the 5′ genomic region: a ~4340 bp deletion (positions ~9020–13,356 in Georgia 2007/1) in four samples and a 2162 bp deletion (positions 17,837–19,998) in one sample. Another strain showed a truncation of 1950 bp at the 3′ end. In Calabria, strains showed a 5137 bp deletion (positions 10,755–15,891) and ~2 kb truncations in the 3′ region. Two strains showed a translocation from the region 1–2244 to positions 188,631–190,584. In vivo characterization of the deleted strain 22489.4_2312/RC/2023 revealed identical disease progression to the wild-type strain, with severe ASF symptoms in inoculated pigs. This study is the first to report natural deleted strains of ASFV in Italy, revealing unique genomic deletions distinct from those in previously known strains. Full article
(This article belongs to the Special Issue Computational Approaches in Mechanisms of Pathogenesis)
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28 pages, 10223 KiB  
Article
Theoretical Study of Sphingomyelinases from Entamoeba histolytica and Trichomonas vaginalis Sheds Light on the Evolution of Enzymes Needed for Survival and Colonization
by Fátima Berenice Ramírez-Montiel, Sairy Yarely Andrade-Guillen, Ana Laura Medina-Nieto, Ángeles Rangel-Serrano, José A. Martínez-Álvarez, Javier de la Mora, Naurú Idalia Vargas-Maya, Claudia Leticia Mendoza-Macías, Felipe Padilla-Vaca and Bernardo Franco
Pathogens 2025, 14(1), 32; https://doi.org/10.3390/pathogens14010032 - 5 Jan 2025
Viewed by 1161
Abstract
The path to survival for pathogenic organisms is not straightforward. Pathogens require a set of enzymes for tissue damage generation and to obtain nourishment, as well as a toolbox full of alternatives to bypass host defense mechanisms. Our group has shown that the [...] Read more.
The path to survival for pathogenic organisms is not straightforward. Pathogens require a set of enzymes for tissue damage generation and to obtain nourishment, as well as a toolbox full of alternatives to bypass host defense mechanisms. Our group has shown that the parasitic protist Entamoeba histolytica encodes for 14 sphingomyelinases (SMases); one of them (acid sphingomyelinase 6, aSMase6) is involved in repairing membrane damage and exhibits hemolytic activity. The enzymatic characterization of aSMase6 has been shown to be activated by magnesium ions but not by zinc, as shown for the human aSMase, and is strongly inhibited by cobalt. However, no structural data are available for the aSMase6 enzyme. In this work, bioinformatic analyses showed that the protist aSMases are diverse enzymes, are evolutionarily related to hemolysins derived from bacteria, and showed a similar overall structure as parasitic, free-living protists and mammalian enzymes. AlphaFold3 models predicted the occupancy of cobalt ions in the active site of the aSMase6 enzyme. Cavity blind docking showed that the substrate is pushed outward of the active site when cobalt is bound instead of magnesium ions. Additionally, the structural models of the aSMase6 of E. histolytica showed a loop that is absent from the rest of the aSMases, suggesting that it may be involved in hemolytic activity, as demonstrated experimentally using the recombinant proteins of aSMase4 and aSMase6. Trichomonas vaginalis enzymes show a putative transmembrane domain and seem functionally different from E. histolytica. This work provides insight into the future biochemical analyses that can show mechanistic features of parasitic protists sphingomyelinases, ultimately rendering these enzymes potential therapeutic targets. Full article
(This article belongs to the Special Issue Computational Approaches in Mechanisms of Pathogenesis)
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32 pages, 15683 KiB  
Article
Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulation to Elucidate the Molecular Targets and Potential Mechanism of Phoenix dactylifera (Ajwa Dates) against Candidiasis
by Mohd Adnan, Arif Jamal Siddiqui, Syed Amir Ashraf, Fevzi Bardakci, Mousa Alreshidi, Riadh Badraoui, Emira Noumi, Bektas Tepe, Manojkumar Sachidanandan and Mitesh Patel
Pathogens 2023, 12(11), 1369; https://doi.org/10.3390/pathogens12111369 - 18 Nov 2023
Cited by 10 | Viewed by 3511
Abstract
Candidiasis, caused by opportunistic fungal pathogens of the Candida genus, poses a significant threat to immunocompromised individuals. Natural compounds derived from medicinal plants have gained attention as potential sources of anti-fungal agents. Ajwa dates (Phoenix dactylifera L.) have been recognized for their [...] Read more.
Candidiasis, caused by opportunistic fungal pathogens of the Candida genus, poses a significant threat to immunocompromised individuals. Natural compounds derived from medicinal plants have gained attention as potential sources of anti-fungal agents. Ajwa dates (Phoenix dactylifera L.) have been recognized for their diverse phytochemical composition and therapeutic potential. In this study, we employed a multi-faceted approach to explore the anti-candidiasis potential of Ajwa dates’ phytochemicals. Utilizing network pharmacology, we constructed an interaction network to elucidate the intricate relationships between Ajwa dates phytoconstituents and the Candida-associated molecular targets of humans. Our analysis revealed key nodes in the network (STAT3, IL-2, PTPRC, STAT1, CASP1, ALB, TP53, TLR4, TNF and PPARG), suggesting the potential modulation of several crucial processes (the regulation of the response to a cytokine stimulus, regulation of the inflammatory response, positive regulation of cytokine production, cellular response to external stimulus, etc.) and fungal pathways (Th17 cell differentiation, the Toll-like receptor signaling pathway, the C-type lectin receptor signaling pathway and necroptosis). To validate these findings, molecular docking studies were conducted, revealing the binding affinities of the phytochemicals towards selected Candida protein targets of humans (ALB–rutin (−9.7 kJ/mol), STAT1–rutin (−9.2 kJ/mol), STAT3–isoquercetin (−8.7 kJ/mol), IL2–β-carotene (−8.5 kJ/mol), CASP1–β-carotene (−8.2 kJ/mol), TP53–isoquercetin (−8.8 kJ/mol), PPARG–luteolin (−8.3 kJ/mol), TNF–βcarotene (−7.7 kJ/mol), TLR4–rutin (−7.4 kJ/mol) and PTPRC–rutin (−7.0 kJ/mol)). Furthermore, molecular dynamics simulations of rutin–ALB and rutin-STAT1 complex were performed to gain insights into the stability and dynamics of the identified ligand–target complexes over time. Overall, the results not only contribute to the understanding of the molecular interactions underlying the anti-fungal potential of specific phytochemicals of Ajwa dates in humans but also provide a rational basis for the development of novel therapeutic strategies against candidiasis in humans. This study underscores the significance of network pharmacology, molecular docking and dynamics simulations in accelerating the discovery of natural products as effective anti-fungal agents. However, further experimental validation of the identified compounds is warranted to translate these findings into practical therapeutic applications. Full article
(This article belongs to the Special Issue Computational Approaches in Mechanisms of Pathogenesis)
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Review

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19 pages, 945 KiB  
Review
Influenza B Virus Vaccine Innovation through Computational Design
by Matthew J. Pekarek and Eric A. Weaver
Pathogens 2024, 13(9), 755; https://doi.org/10.3390/pathogens13090755 - 2 Sep 2024
Viewed by 3109
Abstract
As respiratory pathogens, influenza B viruses (IBVs) cause a significant socioeconomic burden each year. Vaccine and antiviral development for influenza viruses has historically viewed IBVs as a secondary concern to influenza A viruses (IAVs) due to their lack of animal reservoirs compared to [...] Read more.
As respiratory pathogens, influenza B viruses (IBVs) cause a significant socioeconomic burden each year. Vaccine and antiviral development for influenza viruses has historically viewed IBVs as a secondary concern to influenza A viruses (IAVs) due to their lack of animal reservoirs compared to IAVs. However, prior to the global spread of SARS-CoV-2, the seasonal epidemics caused by IBVs were becoming less predictable and inducing more severe disease, especially in high-risk populations. Globally, researchers have begun to recognize the need for improved prevention strategies for IBVs as a primary concern. This review discusses what is known about IBV evolutionary patterns and the effect of the spread of SARS-CoV-2 on these patterns. We also analyze recent advancements in the development of novel vaccines tested against IBVs, highlighting the promise of computational vaccine design strategies when used to target both IBVs and IAVs and explain why these novel strategies can be employed to improve the effectiveness of IBV vaccines. Full article
(This article belongs to the Special Issue Computational Approaches in Mechanisms of Pathogenesis)
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