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A computational model to predict the immune system activation by citrus-derived vaccine adjuvants

Francesco Pappalardo, Epifanio Fichera, Nicoletta Paparone, Alessandro Lombardo, Marzio Pennisi, Giulia Russo, Marco Leotta, Francesco Pappalardo, Alessandro Pedretti, Francesco De Fiore, Santo Motta
2016 Bioinformatics  
Results: We developed a computational framework that provides a complete pipeline capable of predicting the best citrus-derived adjuvants for enhancing the immune system response using, as a target disease  ...  Adjuvants represent a good strategy to overcome such hurdles, indeed they are able to: enhance the immune response; allow antigens sparing; accelerate the specific immune response; and increase vaccine  ...  Acknowledgement The authors would like to thank Dr. Adrian Shepherd for his valuable comments that help to improve the manuscript. Conflict of interest: none declared.  ... 
doi:10.1093/bioinformatics/btw293 pmid:27162187 fatcat:74shdsqotjeirfclslys4o462m

Combining agent based-models and virtual screening techniques to predict the best citrus-derived vaccine adjuvants against human papilloma virus

Marzio Pennisi, Giulia Russo, Silvia Ravalli, Francesco Pappalardo
2017 BMC Bioinformatics  
Conclusions: We built up a computational infrastructure made by a virtual screening approach able to preselect promising citrus derived compounds, and by an agent based model that reproduces HPV dynamics  ...  Results: With the aim to get a stronger immune response against Hpv infection we built an in silico model that delivers a way to predict the best adjuvants and the optimal means of administration to obtain  ...  Here we present an agent based model able to analyze the immune system response induced by adjuvants extracted from citrus, in the context of Hpv infection.  ... 
doi:10.1186/s12859-017-1961-9 pmid:29297294 pmcid:PMC5751416 fatcat:2xlxlyja5ncj5icssrbpzutkzm

Evaluation of the efficacy of RUTI and ID93/GLA-SE vaccines in tuberculosis treatment: in silico trial through UISS-TB simulator [article]

Giulia Russo, Francesco Pappalardo, Miguel A. Juarez, Marzio Pennisi, Pere Joan Cardona, Rhea Coler, Epifanio Fichera, Marco Viceconti
2019 arXiv   pre-print
Here, we present EU - funded STriTuVaD project computational platform able to predict the artificial immunity induced by RUTI and ID93/GLA-SE, two specific tuberculosis vaccines.  ...  Computational modeling represents an extraordinary way to simulate and predict the outcome of vaccination strategies, speeding up the arduous process of vaccine pipeline development and relative time to  ...  ., "A computational model to predict the immune system activation by citrus-derived vaccine adjuvants," Bioinformatics, vol. 32, no. 17, pp. 2672-2680, Sep. 2016.  ... 
arXiv:1911.00325v1 fatcat:nvqq264fpjehfhpamq4hf6isee

Multi-scale Agent-based Models in Immunology. A Short Review

Marzio Pennisi
2021 International Conference on Information and Knowledge Management  
This short review will present some of these agent-based approaches developed for the simulation of diseases and the relative immune system response that also try to explicitly include molecular-level  ...  In the drug discovery pipeline, the lack of multi-scale modeling approaches able of taking into account the observation of an immunological phenomenon from the molecular to the tissue/organism levels represents  ...  This approach has been used in [22] , where the authors predicted the efficacy of some candidate citrus-derived adjuvants (to be used instead of Aluminum salts) for influenza-A vaccines.  ... 
dblp:conf/cikm/Pennisi21 fatcat:oaduhxgzfvhnjdbvxllt7bbvx4

A Review on Herbal Secondary Metabolites Against COVID-19 Focusing on the Genetic Variants of SARS-CoV-2

Mohsen Mohammadi, Yousef Yahyapour, Sina Nasrollahian, Mohammad Hossein Tayefeh-Arbab, Mostafa Javanian, Mohammad Rajabi Fadardi, Seyedeh Nasim Mousavi Kani, Parisa Honarvar Bakeshloo, Roshanak Saghebi, Mehdi Rajabnia, Mehrdad Halaji, Abazar Pournajaf
2022 Jundishapur Journal of Natural Pharmaceutical Products  
Evidence Acquisition: Data were collected through the end of August 2021 by searching PubMed, Scopus, and Google Scholar databases.  ...  Although several vaccines, such as mRNA vaccines, inactivated vaccines, and adenovirus vaccines, have been licensed in several countries, the danger of severe acute respiratory syndrome coronavirus 2 (  ...  A., M. J., M. R. F., S. N. M. K., P. H. B., R. S., and R. R. collected data, contributed to the writing of the manuscript, and revised the final version of the manuscript.  ... 
doi:10.5812/jjnpp-129618 fatcat:dvkn23slfzhznefgx3eg6aekra

Machine Learning-Assisted Screening of Herbal Medicine Extracts as Vaccine Adjuvants

Kou Hioki, Tomoya Hayashi, Yayoi Natsume-Kitatani, Kouji Kobiyama, Burcu Temizoz, Hideo Negishi, Hitomi Kawakami, Hiroyuki Fuchino, Etsushi Kuroda, Cevayir Coban, Nobuo Kawahara, Ken J. Ishii
2022 Frontiers in Immunology  
Adjuvants are important vaccine components, composed of a variety of chemical and biological materials that enhance the vaccine antigen-specific immune responses by stimulating the innate immune cells  ...  It has been developed by empirical methods for decades and considered difficult to choose a single screening method for an ideal vaccine adjuvant, due to their diverse biochemical characteristics, complex  ...  ACKNOWLEDGMENTS We wish to thank all members of the Division of Vaccine Science, IMSUT, for their valuable comments and assistance.  ... 
doi:10.3389/fimmu.2022.847616 pmid:35663999 pmcid:PMC9160479 fatcat:ttvua6enwzgthgim6xpujkz7gy

Generation of digital patients for the simulation of tuberculosis with UISS-TB [article]

Marzio Pennisi, Miguel A. Juarez, Giulia Russo, Marco Viceconti, Francesco Pappalardo
2019 arXiv   pre-print
In parallel, we have extended the Universal Immune System Simulator to include all relevant determinants of such clinical trial, to establish its predictive accuracy against the individual patients recruited  ...  This has been achieved through the the creation of the initial immune system repertoire in a stochastic way, and though the identification of a "vector of features" that combines both biological and pathophysiological  ...  Acknowledgments Authors of this paper acknowledge support from the STriTuVaD project. The STriTuVaD project has been funded N.Ag strain Th1 Th2 IgG TC IL1  ... 
arXiv:1910.12293v1 fatcat:z4ay5mbrxfdgnhdkr6u5q5llt4

A bioinformatics potpourri

Christian Schönbach, Jinyan Li, Lan Ma, Paul Horton, Muhammad Farhan Sjaugi, Shoba Ranganathan
2018 BMC Genomics  
Agent based-model to simulate citrus-derived flavones as vaccine adjuvants against human papilloma virus 16; mouse in vivo result confirmation [43] .  ...  GT-WGS is a distributed whole-genome computing system based on Amazon Web Service cloud computing platform [53] .  ...  • We accept pre-submission inquiries • Our selector tool helps you to find the most relevant journal Submit your next manuscript to BioMed Central and we will help you at every step:  ... 
doi:10.1186/s12864-017-4326-x pmid:29363432 pmcid:PMC5780851 fatcat:i6u2eafvzbf4lawwh2o5b7k42q

Hesperidin and SARS-CoV-2: New Light on the Healthy Function of Citrus Fruits

Paolo Bellavite, Alberto Donzelli
2020 Antioxidants  
Foods are very rich in substances, with a potential beneficial effect on health, and some of these could have an antiviral action or be important in modulating the immune system and in defending cells  ...  There is discussion about the preventive efficacy of vitamin C, at the dose achievable by the diet, but recent reviews suggest that this substance can be useful in the case of strong immune system burden  ...  Acknowledgments: We thank Donatella Sghedoni for her English revision of the manuscript. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/antiox9080742 pmid:32823497 fatcat:rfssw4l5o5frznlotojz5futju

From Bivariate to Multivariate Analysis of Cytometric Data: Overview of Computational Methods and Their Application in Vaccination Studies

Simone Lucchesi, Simone Furini, Donata Medaglini, Annalisa Ciabattini
2020 Vaccines  
Multiparametric flow cytometry is particularly suitable for deep analysis of immune responses after vaccination, as it allows to measure the frequency, the phenotype, and the functional features of antigen-specific  ...  However, the use of these tools has been preferentially restricted to bioinformaticians, while few of them are routinely employed by the biomedical community.  ...  immunization with the adjuvanted-vaccine formulation [57] .  ... 
doi:10.3390/vaccines8010138 pmid:32244919 fatcat:juw6fn4tmjgg3d2jxwt53zycfy

Toward Nanotechnology-Enabled Approaches against the COVID-19 Pandemic

Carsten Weiss, Marie Carriere, Laura Fusco, Ilaria Capua, Jose Angel Regla-Nava, Matteo Pasquali, James A Scott, Flavia Vitale, Mehmet Altay Unal, Cecilia Mattevi, Davide Bedognetti, Arben Merkoçi (+5 others)
2020 ACS Nano  
Moreover, the concept of "nanoimmunity by design" can help us to design materials for immune modulation, either stimulating or suppressing the immune response, which would find applications in the context  ...  In this case, nanomaterials could be used to deliver drugs to the pulmonary system to inhibit interaction between angiotensin-converting enzyme 2 (ACE2) receptors and viral S protein.  ...  Computational models indicate how NPs are taken up by healthy cells or tumor cells, enabling better predictions regarding the pharmacokinetic and pharmacodynamic properties of these materials. 134 For  ... 
doi:10.1021/acsnano.0c03697 pmid:32519842 pmcid:PMC7299399 fatcat:wll5rivadnas3pu5qftk3bvltm

A Multidisciplinary Approach to Coronavirus Disease (COVID-19)

Aliye Gediz Gediz Erturk, Arzu Sahin, Ebru Bati Bati Ay, Emel Pelit, Emine Bagdatli, Irem Kulu, Melek Gul, Seda Mesci, Serpil Eryilmaz, Sirin Oba Oba Ilter, Tuba Yildirim
2021 Molecules  
In addition, we present immunotherapy types, targets, immunotherapy and inflammation/mutations of the virus, immune response, and vaccine issues.  ...  We also highlight computer-aided approaches to develop an anti-COVID-19 molecule.  ...  The authors would like to thank Kathryn Jay Henderson for her valuable contribution of the critical reading of the manuscript. Conflicts of Interest: The authors declare no conflict of interests.  ... 
doi:10.3390/molecules26123526 fatcat:fhnbgpgmifgvhk2c6ijm66643u

Supplementum 239: Annual Congress of the Swiss Society for Allergology and Immunology, jointly organised with the Viral Immunity Symposium

2019 Swiss Medical Weekly  
The neutralizing activity was acquired through somatic mutations and correlated with a slow dissociation rate, a finding that was supported by structural data.  ...  By characterizing a large panel of NZM-specific monoclonal antibodies, we found that, in both patients, the response was polyclonal and targeted different epitopes of the NZM variable region.  ...  P69 Vaccination with nanoparticles combined with micro-adjuvants protects against cancer Active immunotherapy of cancer aims to treat the disease by inducing an effective cellular immune response, in particular  ... 
doi:10.4414/smw.2019.20441 fatcat:m4xmjyglfnea7hsy3sh2z52224

Cancer systems immunology

Nathan E Reticker-Flynn, Edgar G Engleman
2020 eLife  
Armed with these technologies and their associated computational and modeling toolsets, systems biologists have turned their attention to tumor immunology in an effort to understand the precise nature  ...  and consequences of interactions between tumors and the immune system.  ...  Acknowledgements The authors thank members of the Engleman Lab for insightful discussions. This work was supported by NIH grant U54 CA209971 (Engleman).  ... 
doi:10.7554/elife.53839 fatcat:xx4k5vorbraqlkvzjbrjhjw5py

Perspectives for systems biology in the management of tuberculosis

Irina Kontsevaya, Christoph Lange, Patricia Comella-del-Barrio, Cristian Coarfa, Andrew R. DiNardo, Stephen H. Gillespie, Matthias Hauptmann, Christoph Leschczyk, Anna M. Mandalakas, Antal Martinecz, Matthias Merker, Stefan Niemann (+7 others)
2021 European Respiratory Review  
Systems biology is a rapidly expanding field of computational and mathematical analysis and modelling of complex biological systems that can provide insights into mechanisms underlying tuberculosis, identify  ...  Standardised management of tuberculosis may soon be replaced by individualised, precision medicine-guided therapies informed with knowledge provided by the field of systems biology.  ...  Acknowledgements: We thank Henry Krützfeldt ( for the assistance with graphic design of the figure.  ... 
doi:10.1183/16000617.0377-2020 pmid:34039674 fatcat:rboh6jmkazdvpps3vnu4jfj4le
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