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Epitope mapping

Yubao Cui, Lili Yu, Ying Zhou, Li Yang, Chengbo Zhang
Mimotope mapping enables the characterization of allergen epitopes for the development of diagnostic and therapeutic approaches. In the present study, a phage display peptide library was used for mimotope mapping based on the binding of antibodies against the recombinant group 5 allergen from the house dust mite Dermatophagoides farinae (Der f 5), an arthropod that causes indoor allergies worldwide. When three monoclonal anti‑Der f 5 antibodies were used for biopanning, seven mimotopes were identified. Their common subsequence was '‑‑‑[‑A][‑T]W[‑S]H[HSFW][LM][PSKR] [TLV][AST]‑[DP][‑L]‑'...
October 13, 2016: Molecular Medicine Reports
Tiziano Gaiotto, Simon E Hufton
Cross-neutralising monoclonal antibodies against influenza hemagglutinin (HA) are of considerable interest as both therapeutics and diagnostic tools. We have recently described five different single domain antibodies (nanobodies) which share this cross-neutralising activity and suggest their small size, high stability, and cleft binding properties may present distinct advantages over equivalent conventional antibodies. We have used yeast display in combination with deep mutational scanning to give residue level resolution of positions in the antibody-HA interface which are crucial for binding...
2016: PloS One
Jason R Wilson, Zhu Guo, Adrian Reber, Ram P Kamal, Nedzad Music, Shane Gansebom, Yaohui Bai, Min Levine, Paul Carney, Wen-Pin Tzeng, James Stevens, Ian A York
Zoonotic A(H7N9) avian influenza viruses emerged in China in 2013 and continue to be a threat to human public health, having infected over 800 individuals with a mortality rate approaching 40%. Treatment options for people infected with A(H7N9) include the use of neuraminidase (NA) inhibitors. However, like other influenza viruses, A(H7N9) can become resistant to these drugs. The use of monoclonal antibodies is a rapidly developing strategy for controlling influenza virus infection. Here we generated a murine monoclonal antibody (3c10-3) directed against the NA of A(H7N9) and show that prophylactic systemic administration of 3c10-3 fully protected mice from lethal challenge with wild-type A/Anhui/1/2013 (H7N9)...
October 3, 2016: Antiviral Research
Wan-Xiang Xu, Jian Wang, Hai-Ping Tang, Ya-Ping He, Qian-Xi Zhu, Satish K Gupta, Shao-Hua Gu, Qiang Huang, Chao-Neng Ji, Ling-Feng Liu, Gui-Ling Li, Cong-Jian Xu, Yi Xie
To enable rational multi-epitope vaccine and diagnostic antigen design, it is imperative to delineate complete IgG-epitome of the protein. Here, we describe results of IgG-epitome decoding of three proteins from high-risk (HR-) oncogenic human papillomavirus type 58 (HPV58). To reveal their entire epitomes, employing peptide biosynthetic approach, 30 precise linear B-cell epitopes (BCEs) were mapped on E6, E7 and L1 proteins using rabbits antisera to the respective recombinant proteins. Using sequence alignment based on BCE minimal motif, the specificity and conservativeness of each mapped BCE were delineated mainly among known HR-HPVs, including finding 3 broadly antibody cross-reactive BCEs of L1 that each covers almost all HR-HPVs...
October 6, 2016: Scientific Reports
Jiju Mani, Lei Wang, Angela G Hückelhoven, Anita Schmitt, Alma Gedvilaite, Nan Jin, Christian Kleist, Anthony D Ho, Michael Schmitt
Human JC and BK polyomaviruses (JCV/BKV) can establish a latent infection without any clinical symptoms in healthy individuals. In immunocompromised hosts infection or reactivation of JCV and BKV can cause lethal progressive multifocal leukoencephalopathy (PML) and hemorrhagic cystitis, respectively. Vaccination with JCV/BKV derived antigen epitope peptides or adoptive transfer of virus-specific T cells would constitute an elegant approach to clear virus-infected cells. Furthermore, donor leukocyte infusion (DLI) is another therapeutic approach which could be helpful for patients with JCV/BKV infections...
October 1, 2016: Oncotarget
Elisa Pin, Frauke Henjes, Mun-Gwan Hong, Fredrik Wiklund, Patrik Magnusson, Anders Bjartell, Mathias Uhlén, Peter Nilsson, Jochen M Schwenk
There is a demand for novel targets and approaches to diagnose and treat prostate cancer (PCA). In this context, serum and plasma samples from a total of 609 individuals from two independent patient cohorts were screened for IgG reactivity against a sum of 3,833 human protein fragments. Starting from planar protein arrays with 3,786 protein fragments to screen 80 patients with and without PCA diagnosis, 161 fragments (4%) were chosen for further analysis based on their reactivity profiles. Adding 71 antigens from literature, the selection of antigens were corroborated for their reactivity in a set of 550 samples using suspension bead arrays...
October 4, 2016: Journal of Proteome Research
Alexey V Gribenko, Kevin Parris, Lidia Mosyak, Sheng Li, Luke Handke, Julio C Hawkins, Elena Severina, Yury V Matsuka, Annaliesa S Anderson
The Staphylococcus aureus manganese transporter protein MntC is under investigation as a component of a prophylactic S.aureus vaccine. Passive immunization with monoclonal antibodies mAB 305-78-7 and mAB 305-101-8 produced using MntC was shown to significantly reduce S. aureus burden in an infant rat model of infection. Earlier interference mapping suggested that a total of 23 monoclonal antibodies generated against MntC could be subdivided into three interference groups, representing three independent immunogenic regions...
September 2016: PLoS Pathogens
Bing-Fang Chen
AIM: To investigate the associations of different types of pre-S deletions with hepatitis B virus (HBV) genotypes. METHODS: The sequences of the pre-S region, basal core promoter (BCP) mutation, and precore (PC) mutation were examined through direct DNA sequencing or clonal analysis and sequencing in 273 HBV carriers, namely 55 asymptomatic carriers, 55 carriers with chronic hepatitis (CH), 55 with liver cirrhosis (LC), 53 with liver cirrhotic hepatocellular carcinoma (LC-HCC), and 55 with noncirrhotic HCC...
September 21, 2016: World Journal of Gastroenterology: WJG
Deborah Antunes Santos, Mauricio Garcia de Souza Costa, Carlos Roberto Alves, Ernesto Raul Caffarena
Cysteine proteinase B (CPB) is a significant virulence factor for Leishmania infections. Upon processing from its zymogen form, it happens a release of the immunomodulatory CPB C-terminal extension (cyspep) into the cytoplasm of the macrophage. Epitopes derived from this fragment were shown to influence the proportion of lymphocytes CD8+ upon infection, favoring the parasite escaping from the host́s immune system. At present, there is no available structural data of cyspep, which impairs a proper understanding of its biological functions...
September 5, 2016: Journal of Molecular Graphics & Modelling
Afreenish Hassan, Anam Naz, Ayesha Obaid, Rehan Zafar Paracha, Kanwal Naz, Faryal Mehwish Awan, Syed Aun Muhmmad, Hussnain Ahmed Janjua, Jamil Ahmad, Amjad Ali
BACKGROUND: Acinetobacter baumannii has emerged as a significant nosocomial pathogen during the last few years, exhibiting resistance to almost all major classes of antibiotics. Alternative treatment options such as vaccines tend to be most promising and cost effective approaches against this resistant pathogen. In the current study, we have explored the pan-genome of A. baumannii followed by immune-proteomics and reverse vaccinology approaches to identify potential core vaccine targets...
2016: BMC Genomics
Rutger G Woolthuis, Christiaan H van Dorp, Can Keşmir, Rob J de Boer, Michiel van Boven
The evolutionary adaptation of the influenza A virus (IAV) to human antibodies is well characterised. Much less is known about the long-term evolution of cytotoxic T lymphocyte (CTL) epitopes, which are important antigens for clearance of infection. We construct an antigenic map of IAVs of all human subtypes using a compendium of 142 confirmed CTL epitopes, and show that IAV evolved gradually in the period 1932-2015, with infrequent antigenic jumps in the H3N2 subtype. Intriguingly, the number of CTL epitopes per virus decreases with more than one epitope per three years in the H3N2 subtype (from 84 epitopes per virus in 1968 to 64 in 2015), mostly attributed to the loss of HLA-B epitopes...
2016: Scientific Reports
Tony Velkov, Bo Yun, Elena K Schneider, Mohammad A K Azad, Olan Dolezal, Faye C Morris, Roger L Nation, Jiping Wang, Ke Chen, Heidi H Yu, Lv Wang, Philip E Thompson, Kade D Roberts, Jian Li
Polymyxins B and E (i.e., colistin) are a family of naturally occurring lipopeptide antibiotics that are our last line of defense against multidrug resistant (MDR) Gram-negative pathogens. Unfortunately, nephrotoxicity is a dose-limiting factor for polymyxins that limits their clinical utility. Our recent studies demonstrate that polymyxin-induced nephrotoxicity is a result of their extensive accumulation in renal tubular cells. The design and development of safer, novel polymyxin lipopeptides is hampered by our limited understanding of their complex structure-nephrotoxicity relationships...
May 13, 2016: ACS Infectious Diseases
Pragya Yadav, Matthew T Carr, Ruby Yu, Alice Mumbey-Wafula, Linda A Spatz
INTRODUCTION: The Epstein Barr Virus (EBV) has been associated with the autoimmune disease, Systemic Lupus Erythematosus (SLE). EBV nuclear antigen-I (EBNA-1) is the major nuclear protein of EBV. We previously generated an IgG monoclonal antibody (MAb) to EBNA-1, 3D4, and demonstrated that it cross-reacts with double stranded DNA (dsDNA) and binds the 148 amino acid viral binding site (VBS) in the carboxyl region of EBNA-1. The aim of the present study was to characterize another antibody to EBNA-1 that cross-reacts with dsDNA, compare its immunoglobulin genes to 3D4, and finely map the epitope in EBNA-1 that is recognized by these cross-reactive antibodies...
September 2016: Immunity, Inflammation and Disease
Doua F Azzouz, Gabriel V Martin, Fanny Arnoux, Nathalie Balandraud, Thierry Martin, Sylvain Dubucquoi, Eric Hachulla, Dominique Farge-Bancel, Kiet Tiev, Jean Cabane, Nathalie Bardin, Laurent Chiche, Marielle Martin, Eléonore C Caillet, Sami B Kanaan, Jean Robert Harlé, Brigitte Granel, Elisabeth Diot, Jean Roudier, Isabelle Auger, Nathalie C Lambert
In a pilot ProtoArray analysis, we identified 6 proteins out of 9483 recognized by autoantibodies (AAb) from patients with systemic sclerosis (SSc). We further investigated the 6 candidates by ELISA on hundreds of controls and patients, including patients with Systemic Lupus Erythematosus (SLE), known for high sera reactivity and overlapping AAb with SSc. Only 2 of the 6 candidates, Ephrin type-B receptor 2 (EphB2) and Three prime Histone mRNA EXonuclease 1 (THEX1), remained significantly recognized by sera samples from SSc compared to controls (healthy or with rheumatic diseases) with, respectively, 34% versus 14% (P = 2...
2016: PloS One
Alexandra C Walls, M Alejandra Tortorici, Brandon Frenz, Joost Snijder, Wentao Li, Félix A Rey, Frank DiMaio, Berend-Jan Bosch, David Veesler
The threat of a major coronavirus pandemic urges the development of strategies to combat these pathogens. Human coronavirus NL63 (HCoV-NL63) is an α-coronavirus that can cause severe lower-respiratory-tract infections requiring hospitalization. We report here the 3.4-Å-resolution cryo-EM reconstruction of the HCoV-NL63 coronavirus spike glycoprotein trimer, which mediates entry into host cells and is the main target of neutralizing antibodies during infection. The map resolves the extensive glycan shield obstructing the protein surface and, in combination with mass spectrometry, provides a structural framework to understand the accessibility to antibodies...
October 2016: Nature Structural & Molecular Biology
Sindisiwe G Buthelezi, Heini W Dirr, Ereck Chakauya, Rachel Chikwamba, Lennart Martens, Tsepo L Tsekoa, Stoyan H Stoychev, Elien Vandermarliere
Rabies is an acute viral encephalomyelitis in warm-blooded vertebrates, caused by viruses belonging to Rhabdovirus family and genus Lyssavirus. Although rabies is categorised as a neglected disease, the rabies virus (RABV) is the most studied amongst Lyssaviruses which show nearly identical infection patterns. In efforts to improving post-exposure prophylaxis, several anti-rabies monoclonal antibodies (mAbs) targeting the glycoprotein (G protein) sites I, II, III and G5 have been characterized. To explore cross-neutralization capacity of available mAbs and discover new possible B-cell epitopes, we have analyzed all available glycoprotein sequences from Lyssaviruses with a focus on sequence variation and conservation...
November 2016: Virology
Aakanksha Kalra, Paushali Mukherjee, Virander S Chauhan
BACKGROUND: Immunological characterization of potential blood-stage malaria antigens would be a valuable strategy in the development of an effective vaccine. Identifying B and CD4(+) T cell epitopes will be important in understanding the nature of immune response. A previous study has shown that Plasmodium falciparum apical asparagine-rich protein (PfAARP) stimulates immune response and induces potent invasion-inhibitory antibodies. Antibodies to PfAARP provide synergistic effects in inhibition of parasite invasion when used in combination with antibodies to other antigens...
2016: Malaria Journal
Bronwyn Campbell, Helder Cortes, Giada Annoscia, Alessio Giannelli, Antonio Parisi, Maria Stefania Latrofa, Filipe Dantas-Torres, Luís Cardoso, Domenico Otranto
BACKGROUND: Of increasing importance to the medical and veterinary communities is the zoonotic filarioid nematode Onchocerca lupi. Onchocercosis, thus far found in wolves, dogs, cats and humans, is diagnosed via skin snips to detect microfilariae and surgical removal of adults from the eye of the host. These methods are time-consuming, laborious and invasive, highlighting the need for new tools for the diagnosis of O. lupi in susceptible hosts. Symptoms related to the presence of the adults in the eye can range from none apparent to severe, including blindness...
2016: Parasites & Vectors
Noah T Ditto, Ben D Brooks
INTRODUCTION: Surface plasmon resonance (SPR) for affinity/kinetics measurements of drug candidates has been a mainstay application for characterizing drug candidates for many years. Recently, with the growth of monoclonal antibodies (mAbs) as a drug class and the availability of higher-throughput biosensors, the role of label-free biosensors has evolved to include epitope characterization in the early drug discovery process through epitope binning and mapping of mAbs. AREAS COVERED: This manuscript outlines the importance of using epitope characterization early in the drug discovery process and describes a strategy for success in discovering drug leads...
October 2016: Expert Opinion on Drug Discovery
Lyndsey M Muehling, Duy T Mai, William W Kwok, Peter W Heymann, Anna Pomés, Judith A Woodfolk
Rhinovirus (RV) is a major cause of common cold and an important trigger of acute episodes of chronic lung diseases. Antigenic variation across the numerous RV strains results in frequent infections and a lack of durable cross-protection. Because the nature of human CD4(+) T cells that target RV is largely unknown, T cell epitopes of RV capsid proteins were analyzed, and cognate T cells were characterized in healthy subjects and those infected by intranasal challenge. Peptide epitopes of the RV-A16 capsid proteins VP1 and VP2 were identified by peptide/MHC class II tetramer-guided epitope mapping, validated by direct ex vivo enumeration, and interrogated using a variety of in silico methods...
September 2, 2016: Journal of Immunology: Official Journal of the American Association of Immunologists
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