AllerML: Markup language for allergens

Ivanciuc, Ovidiu; Gendel, Steven M.; Power, Trevor D.; Schein, Catherine H.; Braun, Werner

doi:10.1016/j.yrtph.2011.03.006

Cited by 9 publications

(8 citation statements)

References 62 publications

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“…Synthesizing AMP polymers using dendrimer or other AMP nanoparticles to increase the local concentration of the AMP can lower the required dose and combat multidrug-resistant bacteria [133][134][135][136]. (iii) The development of in vitro tests and computational predictions, for example, testing for similarities with allergens, can help to evaluate the immunogenicity and allergenic potential of newly developed AMPs [137], e.g., the basophil activation test [138], cytokine assays [139], lymphocyte activation analysis [140], and Structural Database of Allergenic Proteins (SDAP) [141][142][143]. Although these tools cannot fully predict the allergenic effects of a new AMP in the clinic, they provide a promising preclinical tools for evaluating peptide-based drugs.…”

Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

Development and Challenges of Antimicrobial Peptides for Therapeutic Applications

2020

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More than 3000 antimicrobial peptides (AMPs) have been discovered, seven of which have been approved by the U.S. Food and Drug Administration (FDA). Now commercialized, these seven peptides have mostly been utilized for topical medications, though some have been injected into the body to treat severe bacterial infections. To understand the translational potential for AMPs, we analyzed FDA-approved drugs in the FDA drug database. We examined their physicochemical properties, secondary structures, and mechanisms of action, and compared them with the peptides in the AMP database. All FDA-approved AMPs were discovered in Gram-positive soil bacteria, and 98% of known AMPs also come from natural sources (skin secretions of frogs and toxins from different species). However, AMPs can have undesirable properties as drugs, including instability and toxicity. Thus, the design and construction of effective AMPs require an understanding of the mechanisms of known peptides and their effects on the human body. This review provides an overview to guide the development of AMPs that can potentially be used as antimicrobial drugs.

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Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

Development and Challenges of Antimicrobial Peptides for Therapeutic Applications

2020

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“…Unfortunately, not all of these online databases are regularly updated. In addition, the data are generally not in a detailed format that is easy to incorporate with other databases/methods (Ivanciuc et al, 2011). Moreover, information regarding 3D structure and IgE-epitopes is limited for a large number of allergens.…”

Section: Bioinformatics Approachesmentioning

confidence: 99%

Approaches to assess IgE mediated allergy risks (sensitization and cross-reactivity) from new or modified dietary proteins

Remington¹,

Broekman

Blom³

et al. 2018

Food and Chemical Toxicology

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A B S T R A C TThe development and introduction of new dietary protein sources has the potential to improve food supply sustainability. Understanding the potential allergenicity of these new or modified proteins is crucial to ensure protection of public health. Exposure to new proteins may result in de novo sensitization, with or without clinical allergy, or clinical reactions through cross-reactivity.In this paper we review the potential of current methodologies (in silico, in vitro degradation, in vitro IgE binding, animal models and clinical studies) to address these outcomes for risk assessment purposes for new proteins, and especially to identify and characterise the risk of sensitization for IgE mediated allergy from oral exposure. Existing tools and tests are capable of assessing potential crossreactivity. However, there are few possibilities to assess the hazard due to de novo sensitization. The only methods available are in vivo models, but many limitations exist to use them for assessing risk. We conclude that there is a need to understand which criteria adequately define allergenicity for risk assessment purposes, and from these criteria develop a more suitable battery of tests to distinguish between proteins of high and low allergenicity, which can then be applied to assess new proteins with unknown risks.

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“…In addition, development of software workflow, such as Epidemic Simulation Systems (EPISIM) ( 85 ) has facilitated the semantic model integration for biologically skilled scientists especially with the growing number of available models [over 163 nutrition themed systems biology markup language models (SBML)] that are already available in the Biomodels database ( 86 ). The methodologies to extract actionable knowledge from such rich data and metadata have been facilitated by the development of standards [such as SBML ( 87 ) and more recently Markup language for Allergens (AllerML) ( 88 ), ontologies ( 89 ), for example, Medical Subject Headings (MeSH) ( 90 ), Unified Medical Language System (UMLS) ( 91 ), and Gene Ontology (GO)], and curated specialized databases such as Therapeutic Target Database (TTD) ( 92 ), hepatotoxicity database ( 93 ), drug combination database ( 94 ), Food and Drug administration (FDA) toxicity databases, real-time data entry ( 95 ), and White adipose tissue reference network (WATRefNet) ( 96 ). New bioinformation technologies combine relevant models and data to address important questions whereby the answers reside in the interface between networks.…”

Section: The Current Approaches and The Urgent Need For Paradigm Shifmentioning

confidence: 99%

Modeling-Enabled Systems Nutritional Immunology

et al. 2016

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This review highlights the fundamental role of nutrition in the maintenance of health, the immune response, and disease prevention. Emerging global mechanistic insights in the field of nutritional immunology cannot be gained through reductionist methods alone or by analyzing a single nutrient at a time. We propose to investigate nutritional immunology as a massively interacting system of interconnected multistage and multiscale networks that encompass hidden mechanisms by which nutrition, microbiome, metabolism, genetic predisposition, and the immune system interact to delineate health and disease. The review sets an unconventional path to apply complex science methodologies to nutritional immunology research, discovery, and development through “use cases” centered around the impact of nutrition on the gut microbiome and immune responses. Our systems nutritional immunology analyses, which include modeling and informatics methodologies in combination with pre-clinical and clinical studies, have the potential to discover emerging systems-wide properties at the interface of the immune system, nutrition, microbiome, and metabolism.

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AllerML: Markup language for allergens

Cited by 9 publications

References 62 publications

Development and Challenges of Antimicrobial Peptides for Therapeutic Applications

Development and Challenges of Antimicrobial Peptides for Therapeutic Applications

Approaches to assess IgE mediated allergy risks (sensitization and cross-reactivity) from new or modified dietary proteins

Modeling-Enabled Systems Nutritional Immunology

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