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Structural and Thermodynamic Approach to Peptide Immunogenicity

Carlos J. Camacho, Yasuhiro Katsumata, Dana P. Ascherman, Thomas Lengauer
2008 PLoS Computational Biology  
Collectively, these studies provide insight pertinent to the structural basis of immunogenicity and, at the same time, validate this form of thermodynamic and molecular modeling as an approach to probe  ...  However, it is well known that relatively unstable peptides bearing only partial structural resemblance to the native protein can trigger antibodies recognizing higher-order structures found in the native  ...  Acknowledgments The authors wish to thank William Ridgway and Olivera Finn for critical review of this manuscript. The authors also acknowledge Alpay Temiz for technical assistance.  ... 
doi:10.1371/journal.pcbi.1000231 pmid:19023401 pmcid:PMC2577884 fatcat:ghip7io2hrhd5ay75yeexkyg7i

Increased Immunogenicity of an Anchor-Modified Tumor-Associated Antigen Is Due to the Enhanced Stability of the Peptide/MHC Complex: Implications for Vaccine Design

O. Y. Borbulevych, T. K. Baxter, Z. Yu, N. P. Restifo, B. M. Baker
2005 Journal of Immunology  
Jue Chen and Eva Skrzypczak-Jankun, John Clemens, Tommy Schad, the staff of the Argonne Structural Biology Center, and Joe Miller of Shamrock Structures for assistance. Disclosures B. M.  ...  Baker has a patent pending for the use of ␤-hydroxy amino acids at the first primary anchor for increasing peptide/MHC-I stability.  ...  Thus, our results suggest an approach for engineering the gp100 209 peptide to achieve further gains in peptide/MHC stability and, potentially, immunogenicity.  ... 
doi:10.4049/jimmunol.174.8.4812 pmid:15814707 pmcid:PMC2241749 fatcat:vmsfopsi6vb3ho6ondzqedoij4

On the Meaning of Affinity Limits in B-Cell Epitope Prediction for Antipeptide Antibody-Mediated Immunity

Salvador Eugenio C. Caoili
2012 Advances in Bioinformatics  
B-cell epitope prediction aims to aid the design of peptide-based immunogens (e.g., vaccines) for eliciting antipeptide antibodies that protect against disease, but such antibodies fail to confer protection  ...  Hence, the Immune Epitope Database (IEDB) was searched to obtain published thermodynamic and kinetic data on binding interactions of antipeptide antibodies.  ...  insofar as thermodynamically unfavorable structural adjustments would be unnecessary for the protein to mimic the peptide.  ... 
doi:10.1155/2012/346765 pmid:23209458 pmcid:PMC3505629 fatcat:st66fy2hirdsboxx3v2hxcg2uy

EpIC: a rational pipeline for epitope immunogenicity characterization: Fig. 1

Kristen Marciniuk, Brett Trost, Scott Napper
2015 Bioinformatics  
Efforts to develop peptide-based vaccines, in particular those requiring site-specific targeting of self-proteins, rely on the ability to optimize the immunogenicity of the peptide epitopes.  ...  To improve on this we present the program EpIC, which enables high-throughput prediction of peptide immunogenicity based on the endogenous occurrence of B-cell epitopes within native protein sequences.  ...  The Canadian Institutes of Health Research and the Saskatchewan Health Research Foundation provide funding to K.M. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btv136 pmid:25750418 pmcid:PMC4495294 fatcat:4selubhpgfgyrh4m5jdie3zh6u

Computational methods in preformulation study for pharmaceutical solid dosage forms of therapeutic proteins

Sutapa Biswas Majee, Gopa Roy Biswas
2017 Physical Sciences Reviews  
The objective of the present review article is to focus on the various analytical methods and computational approaches used in the study of thermodynamic stability and aggregation tendency of therapeutic  ...  proteins, with an aim to develop optimal and marketable formulation.  ...  Computational tools in assessment of immunogenicity of therapeutic proteins Therapeutic antibodies, exogenous enzymes, signalling peptides of well-defined structure and function can be immunogenic, if  ... 
doi:10.1515/psr-2017-0007 fatcat:gn3ea3xgmzaalhteh2m3cpia5e

Quantitative Prediction of the Landscape of T Cell Epitope Immunogenicity in Sequence Space

Masato Ogishi, Hiroshi Yotsuyanagi
2019 Frontiers in Immunology  
This study indicates that targeting of epitopes by human adaptive immunity is to some extent directed by defined thermodynamic principles.  ...  To quantitatively describe epitope immunogenicity, here we propose a supervised machine learning framework generating probabilistic estimates of immunogenicity, termed "immunogenicity scores," based on  ...  ACKNOWLEDGMENTS We thank Ryo Ueno and Kazuki Nagashima for helpful discussions.  ... 
doi:10.3389/fimmu.2019.00827 pmid:31057550 pmcid:PMC6477061 fatcat:uioy2omhr5aphafdofpvz3z2oi

Screening for peptide drugs from the natural repertoire of biodiverse protein folds

Paul M Watt
2006 Nature Biotechnology  
Libraries of such peptides (referred to hereafter as phylomers) comprise both random and structured peptides encoded by natural genes of diverse bacterial genomes.  ...  This perspective outlines an alternative approach developed in my laboratory based on libraries of natural, highly structured peptides that may offer new opportunities for designing effective and specific  ...  Phylomer immunogenicity An obvious risk of the phylomer approach is that because the peptides are derived from foreign sources, they might be expected to have a higher chance of immunogenicity than human  ... 
doi:10.1038/nbt1190 pmid:16465163 fatcat:7l6sowxjpvdtdfmwduj6oqq4m4

Affinity selection of epitope-based vaccines using a bacteriophage virus-like particle platform

John P O'Rourke, David S Peabody, Bryce Chackerian
2015 Current Opinion in Virology  
This technology integrates epitope discovery and immunization functions into a single platform.  ...  Display of epitopes on virus-like particles (VLPs) is a highly effective technique for enhancing the immunogenicity of antigens that are poorly immunogenic in their native context.  ...  Acknowledgements This work has been funded by the National Institutes of Health (R01 AI083305 to B.C. and R01 GM042901 to D.S.P.).  ... 
doi:10.1016/j.coviro.2015.03.005 pmid:25829254 pmcid:PMC4456241 fatcat:6uojjijjyvaffe7wmawyyb6ljy

B-cell epitope prediction for peptide-based vaccine design: towards a paradigm of biological outcomes for global health

Salvador Eugenio C Caoili
2011 Immunome Research  
To better support peptide-based vaccine design, B-cell epitope prediction would entail individualized quantitative estimation of biological outcomes relevant to safety and efficacy.  ...  of continuous outcome variables, and (2) failure to explicitly model biological consequences of immunization that are relevant to practical considerations of safety and efficacy.  ...  Such a link is found in structural energetics, which relates the structure of biomolecules to the thermodynamics of their folding and binding [141] [142] [143] .  ... 
doi:10.4172/1745-7580.1000044 fatcat:otnjbotewbbv7ottqopuvnadtu

Optimization algorithms for functional deimmunization of therapeutic proteins

Andrew S Parker, Wei Zheng, Karl E Griswold, Chris Bailey-Kellogg
2010 BMC Bioinformatics  
The output is a scored list of sets of point mutations predicted to reduce the protein's immunogenicity while maintaining structure and function.  ...  In contrast with existing methods, those described here integrate analysis of immunogenicity and stability/ activity, are broadly applicable to any protein class, guarantee global optimality, and provide  ...  Acknowledgements This work is supported in part by US NSF grant IIS-0444544 and an Alfred P. Sloan Foundation Fellowship to CBK, and a Neukom Institute CompX grant to CBK and KEG. Author Details  ... 
doi:10.1186/1471-2105-11-180 pmid:20380721 pmcid:PMC2873530 fatcat:whee4ncza5ctlattzqgvdkpina

Conformational Flexibility in Designing Peptides for Immunology: The Molecular Dynamics Approach

Athanassios Stavrakoudis
2010 Current Computer - Aided Drug Design  
Designing new and optimal peptide vaccines is one of the hottest challenges of the 21 st century science and it brings together researchers from different fields.  ...  Present review is dedicated to the recent contributions in applications of molecular dynamics simulations in peptide design for immunological purposes, such as B or T cell epitopes.  ...  Thermodynamics of Peptide's Immunogenicity MD simulations have been also used in order to study the thermodynamics of peptide's immunogenicity.  ... 
doi:10.2174/157340910791760073 pmid:20412039 fatcat:4a65bz65kvaidewqy7vjo3vtye

Predicting Cross-Reactivity and Antigen Specificity of T Cell Receptors

Chloe H. Lee, Mariolina Salio, Giorgio Napolitani, Graham Ogg, Alison Simmons, Hashem Koohy
2020 Frontiers in Immunology  
We discuss current experimental and computational approaches to investigate cross-reactivity and antigen-specificity of TCRs and highlight how integrating kinetic, biophysical and structural features may  ...  Adaptive immune recognition is mediated by specific interactions between heterodimeric T cell receptors (TCRs) and their cognate peptide-MHC (pMHC) ligands, and the methods to accurately predict TCR:pMHC  ...  From IEDB, 204 immunogenic and 232 non-immunogenic (self-peptides from MHC ligand elution experiment with no known immunogenicity) for H-2D b , and 372 immunogenic and 201 non-immunogenic peptides for  ... 
doi:10.3389/fimmu.2020.565096 pmid:33193332 pmcid:PMC7642207 fatcat:kj6iprpjjrbw5lt56nzqbeqady

Predicting Immunogenicity Risk in Biopharmaceuticals

Nikolet Doneva, Irini Doytchinova, Ivan Dimitrov
2021 Symmetry  
The direct experimental approaches are sometimes expensive and time consuming, or their results need to be confirmed.  ...  The assessment of immunogenicity of biopharmaceuticals is a crucial step in the process of their development. Immunogenicity is related to the activation of adaptive immunity.  ...  The structure-based methods can be used to analyze the impact on the binding affinity and immunogenicity of MHC-binding peptides after phosphorylation [22] , citrullination [23] , and glycosylation  ... 
doi:10.3390/sym13030388 fatcat:yfgas5oagrgflik46woqv6as2u

Exchanging Murine and Human Immunoglobulin Constant Chains Affects the Kinetics and Thermodynamics of Antigen Binding and Chimeric Antibody Autoreactivity

Marcela Torres, Narcis Fernandez-Fuentes, András Fiser, Arturo Casadevall, Wasif Khan
2007 PLoS ONE  
The interaction of a 12-mer peptide mimetic with monoclonal antibody (mAb) 18B7 to Cryptococcus neoformans glucuronoxylomannan, and its chimeric (ch) and deglycosylated forms were studied by surface plasmon  ...  Consequently, we investigated whether heterologous C-regions from mice and humans affected specificity and affinity, and determined the contribution of C H glycosylation to antigen binding.  ...  Fajardo and Dr. Joshua D. Nosanchuk for critical review of the manuscript.  ... 
doi:10.1371/journal.pone.0001310 pmid:18074033 pmcid:PMC2110899 fatcat:fudorp3bznd5liyeocqqqgd7ke

Engineering virus-like particles as vaccine platforms

Kathryn M Frietze, David S Peabody, Bryce Chackerian
2016 Current Opinion in Virology  
Here, we review selected VLP vaccine platforms, highlight efforts to improve these platforms through structure-informed rational design, and point to areas of future research that will assist in these  ...  Virus-like particles (VLPs) have been utilized as vaccine platforms to increase the immunogenicity of heterologous antigens.  ...  Acknowledgments This work has been funded by the National Institutes of Health (R01 AI083305 to BC and R01 GM042901 to DSP).  ... 
doi:10.1016/j.coviro.2016.03.001 pmid:27039982 pmcid:PMC4983494 fatcat:be4c4k4gvff4pfecmzn7ol2k74
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