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1.
Cell Rep ; 38(5): 110303, 2022 02 01.
Article in English | MEDLINE | ID: mdl-35108544

ABSTRACT

Across the animal kingdom, multivalency discriminates antibodies from all other immunoglobulin superfamily members. The evolutionary forces conserving multivalency above other structural hallmarks of antibodies remain, however, incompletely defined. Here, we engineer monovalent either Fc-competent or -deficient antibody formats to investigate mechanisms of protection of neutralizing antibodies (nAbs) and non-neutralizing antibodies (nnAbs) in virus-infected mice. Antibody bivalency enables the tethering of virions to the infected cell surface, inhibits the release of virions in cell culture, and suppresses viral loads in vivo independently of Fc gamma receptor (FcγR) interactions. In return, monovalent antibody formats either do not inhibit virion release and fail to protect in vivo or their protective efficacy is largely FcγR dependent. Protection in mice correlates with virus-release-inhibiting activity of nAb and nnAb rather than with their neutralizing capacity. These observations provide mechanistic insights into the evolutionary conservation of antibody bivalency and help refining correlates of nnAb protection for vaccine development.


Subject(s)
Antibodies, Viral/pharmacology , Antiviral Agents/pharmacology , HIV Antibodies/pharmacology , Receptors, Fc/drug effects , Animals , Antibodies, Neutralizing/immunology , Antibodies, Neutralizing/pharmacology , Antibodies, Viral/immunology , Epitopes/drug effects , Epitopes/immunology , HIV Antibodies/immunology , Immunoglobulin G/drug effects , Immunoglobulin G/immunology , Mice, Inbred C57BL , Receptors, IgG/drug effects , Receptors, IgG/immunology
2.
Bioorg Chem ; 116: 105382, 2021 11.
Article in English | MEDLINE | ID: mdl-34598087

ABSTRACT

The bone morphogenetic protein-2 (BMP-2) is an essential regulator of bone formation and remodeling, which has also been implicated in the pathogenesis of osteoarthritis and its closely related chondrocyte senescence. The BMP-2 uses a conformational wrist epitope and a linear knuckle epitope to interact with type-I (BMPR-I) and type-II (BMPR-II) receptors, respectively. Previously, the knuckle epitope has been intensely studied, but the wrist epitope still remains largely unexplored due to its discontinuous nature. In the present work, the intermolecular interaction of BMP-2 with BMPR-I was investigated systematically at structural, energetic and dynamic levels. Three discrete hotspots that represent the key BMPR-I recognition sites of BMP-2 were identified; they are spatially dispersed over the two monomers of BMP-2 dimer and totally account for 83.5 % binding potency of BMP-2 to BMPR-I (hotspot 1: residues 49-70 in monomer 1; hotspot 2: residues 24-31 in monomer 2; hotspot 3: residues 88-107 in monomer 2). Therefore, we defined the three discrete hotspot sites as the core region of wrist epitope; their contribution to the binding increases in the order: hotspot 2 < hotspot 3 < hotspot 1. We demonstrated that the primary hotspot 1 site has a native U-shaped conformation in the full-length BMP-2 protein context, but it cannot maintain in the native conformation when split from the context to obtain a free hotspot-1 peptide, thus largely impairing its binding potency to BMPR-I. We further employed disulfide-bonded cyclization and head-to-tail cyclization to constrain the peptide conformation, and found that only the former can effectively constrain the peptide into native conformation, thus considerably improving its binding affinity to BMPR-I, whereas the latter totally disorders the native conformation, thus rendering the peptide as a full nonbinder of BMPR-I.


Subject(s)
Bone Morphogenetic Protein 2/antagonists & inhibitors , Chondrocytes/drug effects , Drug Design , Peptides/pharmacology , Bone Morphogenetic Protein 2/metabolism , Chondrocytes/metabolism , Dose-Response Relationship, Drug , Epitopes/drug effects , Humans , Molecular Structure , Osteogenesis/drug effects , Peptides/chemical synthesis , Peptides/chemistry , Structure-Activity Relationship
3.
Pediatr Infect Dis J ; 40(5S): S35-S39, 2021 05 01.
Article in English | MEDLINE | ID: mdl-34042909

ABSTRACT

Respiratory syncytial virus (RSV) is the leading cause of hospitalizations in infants worldwide. Palivizumab, a humanized monoclonal antibody against the RSV F protein, is the only licensed agent for prevention of severe RSV infection in high-risk infants. Palivizumab is administered intramuscularly, every month during the RSV season, usually 5 doses are required. In recent years, the resolution of the structure of the RSV F protein, with identification of potent neutralizing epitopes, and new technologies for production of monoclonal antibodies (mAbs) have facilitated the development of new alternative strategies for the prevention of RSV infections. One promising approach is a new generation of mAbs directed to new neutralizing epitopes and with prolonged half life. These enhanced mAbs are expected to provide adequate protection during the complete RSV season with a single intramuscular (IM) dose. The long-term goal of this approach is to provide passive immunization for the prevention of RSV lower respiratory tract infection to all infants (preterm and full term) in the first months of life before their initial exposure to RSV.


Subject(s)
Antibodies, Monoclonal, Humanized/pharmacology , Antibodies, Monoclonal, Humanized/therapeutic use , Respiratory Syncytial Virus Infections/prevention & control , Respiratory Syncytial Virus, Human/drug effects , Viral Fusion Proteins , Antibodies, Monoclonal, Humanized/history , Clinical Trials as Topic , Epitopes/drug effects , Half-Life , History, 20th Century , History, 21st Century , Humans , Immunization, Passive/methods , Infant , Infant, Newborn
4.
Int J Biol Macromol ; 175: 535-543, 2021 Apr 01.
Article in English | MEDLINE | ID: mdl-33529635

ABSTRACT

In diabetes mellitus, hyperglycemia mediated non-enzymatic glycosylation of proteins results in the pathogenesis of diabetes-associated secondary complications via the generation of advanced glycation end products (AGEs). The focus of this study is to reveal the immunological aspects of methylglyoxal (MG) mediated glycation of fibrinogen protein. The induced immunogenicity of modified fibrinogen is analyzed by direct binding and inhibition ELISA. Direct binding ELISA confirmed that MG glycated fibrinogen (MG-Fib) is highly immunogenic and induces a high titer of antibodies in comparison to its native analog. Cross-reactivity and antigen-binding specificity of induced antibodies were confirmed by inhibition ELISA. The enhanced affinity of immunoglobulin G (IgG) from immunized rabbits' sera and MG glycated fibrinogen is probably the aftermath of neo-epitopes generation in the native structure of protein upon modification. Thus, we deduce that under the glycative stress, MG-mediated structural alterations in fibrinogen could induce the generation of antibodies which might serve as a potential biomarker in diabetes mellitus and its associated secondary disorders.


Subject(s)
Adaptive Immunity/immunology , Fibrinogen/immunology , Pyruvaldehyde/chemistry , Adaptive Immunity/drug effects , Animals , Autoantibodies/immunology , Cross Reactions/immunology , Diabetes Mellitus, Type 2/blood , Enzyme-Linked Immunosorbent Assay/methods , Epitopes/drug effects , Epitopes/immunology , Female , Fibrinogen/metabolism , Glycation End Products, Advanced/metabolism , Glycosylation/drug effects , Hyperglycemia/blood , Immune Sera/immunology , Immunoglobulin G/immunology , Pyruvaldehyde/metabolism , Rabbits
5.
Sci Rep ; 11(1): 1914, 2021 01 21.
Article in English | MEDLINE | ID: mdl-33479293

ABSTRACT

Acinetobacter baumannii is a serious health threat with a high mortality rate. We have already reported prophylactic effects of IgYs raised against OmpA and Omp34 as well as against inactivated whole-cell (IWC) of A. baumannii in a murine pneumonia model. However, the infection was exacerbated in the mice group that received IgYs raised against the combination of OmpA and Omp34. The current study was conducted to propose reasons for the observed antibody-dependent enhancement (ADE) in addition to the therapeutic effect of specific IgYs in the murine pneumonia model. This phenomenon was hypothetically attributed to topologically inaccessible similar epitopes of OmpA and Omp34 sharing similarity with peptides of mice proteins. In silico analyses revealed that some inaccessible peptides of OmpA shared similarity with peptides of Omp34 and Mus musculus. Specific anti-OmpA and anti-Omp34 IgYs cross-reacted with Omp34 and OmpA respectively. Specific IgYs showed different protectivity against A. baumannii AbI101 in the murine pneumonia model. IgYs triggered against OmpA or IWC of A. baumannii were the most protective antibodies. IgY triggered against Omp34 is ranked next after those against OmpA. The lowest protection was observed in mice received IgYs raised against the combination of rOmpA and rOmp34. In conclusion, specific IgYs against OmpA, Omp34, and IWC of A. baumannii could serve as novel biotherapeutics against A. baumannii pneumonia.


Subject(s)
Acinetobacter baumannii/drug effects , Immunoglobulins/immunology , Pneumonia/drug therapy , Vaccines/immunology , Acinetobacter baumannii/immunology , Acinetobacter baumannii/pathogenicity , Animals , Antibody-Dependent Enhancement/drug effects , Antibody-Dependent Enhancement/immunology , Bacterial Outer Membrane Proteins/antagonists & inhibitors , Bacterial Outer Membrane Proteins/immunology , Disease Models, Animal , Egg Yolk/chemistry , Egg Yolk/immunology , Epitopes/drug effects , Epitopes/immunology , Humans , Immunoglobulins/pharmacology , Mice , Pneumonia/genetics , Pneumonia/immunology , Pneumonia/microbiology , Vaccines/pharmacology
6.
Cells ; 10(1)2021 01 07.
Article in English | MEDLINE | ID: mdl-33430453

ABSTRACT

Gold nanoparticles (AuNPs) have demonstrated outstanding performance in many biomedical applications. Their safety is recognised; however, their effects on the immune system remain ill defined. Antigen-presenting cells (APCs) are immune cells specialised in sensing external stimulus and in capturing exogenous materials then delivering signals for the immune responses. We used primary macrophages (Ms) and dendritic cells (DCs) of mice as an APC model. Whereas AuNPs did not alter significantly Ms and DCs functions, the exposure to AuNPs affected differently Ms and DCs in their responses to subsequent stimulations. The secretion of inflammatory molecules like cytokines (IL-6, TNF-α), chemokine (MCP-1), and reactive oxygen species (ROS) were altered differently in Ms and DCs. Furthermore, the metabolic activity of Ms was affected with the increase of mitochondrial respiration and glycolysis, while only a minor effect was seen on DCs. Antigen presentation to T cells increased when DCs were exposed to AuNPs leading to stronger Th1, Th2, and Th17 responses. In conclusion, our data provide new insights into the complexity of the effects of AuNPs on the immune system. Although AuNPs may be considered as devoid of significant effect, they may induce discrete modifications on some functions that can differ among the immune cells.


Subject(s)
Dendritic Cells/metabolism , Gold/pharmacology , Macrophages/metabolism , Metal Nanoparticles/chemistry , Animals , Antigen-Presenting Cells/cytology , Antigen-Presenting Cells/drug effects , Antigen-Presenting Cells/metabolism , Biomarkers/metabolism , Cell Line , Cell Membrane/drug effects , Cell Membrane/metabolism , Cell Survival/drug effects , Dendritic Cells/drug effects , Epitopes/drug effects , Glycolysis/drug effects , Gold/toxicity , Macrophages/drug effects , Metal Nanoparticles/toxicity , Mice, Inbred C57BL , Mitochondria/drug effects , Mitochondria/metabolism , Phagocytosis/drug effects , Signal Transduction/drug effects , T-Lymphocytes/drug effects , T-Lymphocytes/metabolism
7.
Macromol Biosci ; 21(1): e2000234, 2021 01.
Article in English | MEDLINE | ID: mdl-33043585

ABSTRACT

The highly complex nature of spinal cord injuries (SCIs) requires design of novel biomaterials that can stimulate cellular regeneration and functional recovery. Promising SCI treatments use biomaterial scaffolds, which provide bioactive cues to the cells in order to trigger neural regeneration in the spinal cord. In this work, the use of peptide nanofibers is demonstrated, presenting protein binding and cellular adhesion epitopes in a rat model of SCI. The self-assembling peptide molecules are designed to form nanofibers, which display heparan sulfate mimetic and laminin mimetic epitopes to the cells in the spinal cord. These neuroactive nanofibers are found to support adhesion and viability of dorsal root ganglion neurons as well as neurite outgrowth in vitro and enhance tissue integrity after 6 weeks of injury in vivo. Treatment with the peptide nanofiber scaffolds also show significant behavioral improvement. These results demonstrate that it is possible to facilitate regeneration especially in the white matter of the spinal cord, which is usually damaged during the accidents using bioactive 3D nanostructures displaying high densities of laminin and heparan sulfate-mimetic epitopes on their surfaces.


Subject(s)
Nanofibers/chemistry , Peptides/pharmacology , Spinal Cord Injuries/drug therapy , Spinal Cord/drug effects , White Matter/growth & development , Animals , Cell Adhesion/drug effects , Cell Survival/drug effects , Disease Models, Animal , Epitopes/drug effects , Ganglia, Spinal/drug effects , Humans , Nerve Regeneration/drug effects , Neurons/drug effects , Peptides/chemistry , Protein Binding/drug effects , Rats , Spinal Cord/growth & development , Spinal Cord/pathology , Spinal Cord Injuries/pathology , White Matter/drug effects
8.
Biotechnol Lett ; 43(2): 369-382, 2021 Feb.
Article in English | MEDLINE | ID: mdl-33141321

ABSTRACT

OBJECTIVE: Currently, there are two categories of epidermal growth factor receptor (EGFR) antagonists, small molecule antagonists and anti-EGFR antibodies. In the current study, we developed a new EGFR antagonist employing the anti-idiotypic antibodies strategy. RESULTS: First, using EGF as an antigen, through a series of immunological protocols and hybridoma technology, we obtained an anti-idiotypic antibody against EGF receptor-binding epitopes. On this basis, we screened and characterized the anti-idiotype antibodies against EGFR through competitive ELISA, co-localization analysis, competitive receptor binding analysis, and immunofluorescence. Finally, an internal image anti-idiotype antibody called FG8 was successfully prepared. Experiment result shows that FG8 inhibits EGFR-mediated signaling pathways in vitro. Additionally, FG8 inhibits liver tumor cell proliferation as well as induces tumor cell apoptosis. CONCLUSIONS: The present study suggests that FG8 is a potential therapeutic agent for liver cancer. In addition, this study provides a novel method for the preparation of EGFR antagonists.


Subject(s)
Antibodies, Anti-Idiotypic/biosynthesis , Antineoplastic Agents/pharmacology , Liver Neoplasms/drug therapy , Antibodies, Anti-Idiotypic/drug effects , Antibodies, Anti-Idiotypic/immunology , Antineoplastic Agents/chemistry , Apoptosis/drug effects , Binding, Competitive/drug effects , Cell Line, Tumor , Cell Proliferation/drug effects , Enzyme-Linked Immunosorbent Assay , Epitopes/drug effects , Epitopes/genetics , ErbB Receptors/antagonists & inhibitors , ErbB Receptors/genetics , ErbB Receptors/immunology , Humans , Liver Neoplasms/genetics , Liver Neoplasms/immunology , Liver Neoplasms/pathology , Protein Binding/genetics , Signal Transduction/drug effects
9.
Brain Res ; 1747: 147038, 2020 11 15.
Article in English | MEDLINE | ID: mdl-32738231

ABSTRACT

Cognitive impairment is a significant sequela of traumatic brain injury (TBI) especially blast induced traumatic brain injury (bTBI), which is characterized by rapid impairments of learning and memory ability. Although several neuroprotective agents have been postulated as promising drugs for bTBI in animal studies, very few ideal therapeutic options exist to improve cognitive impairment following bTBI. Thymosin α1(Tα1), a 28-amino-acid protein that possesses immunomodulatory functions, has exhibited beneficial effects in the treatment of infectious diseases, immunodeficiency diseases and cancers. However, it remains unclear whether Tα1 has a therapeutic role in bTBI. Thus, we hypothesized that Tα1 administration could reverse the outcomes of bTBI. The blast induced TBI (bTBI) rat model was established with the compressed gas driven blast injury model system. A consecutive Tα1 therapy (in 1 ml saline, twice a day) at a dose of 200 µg/kg or normal saline (NS) (1 ml, twice a day) for 3 days or 2 weeks was performed. Utilizing our newly designed bTBI model, we investigated the beneficial effects of Tα1 therapy on rats exposed to bTBI including: cognitive functions, general histology, regulatory T (Treg) cells, edema, inflammation reactions and the expression and phosphorylation level of tau via Morris Water Maze test (MWM test), HE staining, flow cytometry, brain water content (BWC) calculation, IL-6 assay and Western blotting, respectively. Tα1 treatment seemed to reduce the 24-hour mortality, albeit with no statistical significance. Moreover, Tα1 treatment markedly improved cognitive dysfunction by decreasing the escape latency in the acquisition phase, and increasing the crossing numbers in the probe phase of MWM test. More interestingly, Tα1 significantly inhibited tau phosphorylation at the Thr205 epitope, but not at the Ser404 and Ser262 epitopes. Tα1 increased the percentage of Treg cells and inhibited plasma IL-6 production on 3d post bTBI. Moreover, Tα1 suppressed brain edema as demonstrated by decrease of BWC. However, there was a lack of obvious change in histopathology in the brain upon Tα1 treatment. This is the first study showing that Tα1 improves neurological deficits after bTBI in rats, which is potentially related to the inhibition of tau phosphorylation at the Thr205 epitope, increased Treg cells and decreased inflammatory reactions and brain edema.


Subject(s)
Blast Injuries/complications , Brain Injuries, Traumatic/complications , Brain/drug effects , Cognition/drug effects , Cognitive Dysfunction/drug therapy , Neuroprotective Agents/therapeutic use , Thymalfasin/therapeutic use , tau Proteins/metabolism , Animals , Blast Injuries/metabolism , Brain/metabolism , Brain Injuries, Traumatic/metabolism , Cognitive Dysfunction/etiology , Cognitive Dysfunction/metabolism , Disease Models, Animal , Epitopes/drug effects , Hippocampus/drug effects , Hippocampus/metabolism , Interleukin-6/metabolism , Maze Learning/drug effects , Neuroprotective Agents/pharmacology , Phosphorylation/drug effects , Rats , Thymalfasin/pharmacology , Treatment Outcome
10.
Nanomedicine ; 29: 102255, 2020 10.
Article in English | MEDLINE | ID: mdl-32615339

ABSTRACT

The V1V2 loop of the Env protein is a major target for HIV-1 vaccine development because in multiple studies antibodies to this region correlated with protection. Although SAPNs expressed in E. coli elicited anti-V1V2 antibodies, the Env protein is heavily glycosylated. In this study the technology has been adapted for expression in mammalian cells. SAPNs containing a V1V2 loop from a B-subtype transmitter/founder virus were expressed in E. coli, ExpiCHO, and Expi293 cells. Independent of the expression host, particles were well-formed. All SAPNs raised high titers of V1V2-specific antibodies, however, SAPNE.coli induced a mainly anti-V1 response, while SAPNExpiCHO and SAPNExpi293 induced a predominantly anti-V2 response. In an ADCP assay, sera from animals immunized with the SAPNExpiCHO or SAPNExpi293 induced a significant increase in phagocytic activity. This novel way of producing SAPNs displaying glycosylated epitopes could increase the antibody titer, functional activity, and shift the immune response towards the desired pathway.


Subject(s)
HIV Infections/genetics , HIV-1/genetics , Immunity/genetics , Nanoparticles/chemistry , Animals , Antibodies, Monoclonal/genetics , Antibodies, Monoclonal/immunology , Antibodies, Neutralizing/drug effects , Antibodies, Neutralizing/immunology , Epitopes/drug effects , Epitopes/immunology , Escherichia coli/genetics , Gene Products, env/genetics , Gene Products, env/immunology , HIV Infections/immunology , HIV Infections/virology , HIV-1/immunology , HIV-1/pathogenicity , Humans , Immunity/immunology , Immunization
11.
Sci Adv ; 6(5): eaax2285, 2020 01.
Article in English | MEDLINE | ID: mdl-32064333

ABSTRACT

To be optimally effective, peptide-based vaccines need to be administered with adjuvants. Many currently available adjuvants are toxic, not biodegradable; they invariably invoke adverse reactions, including allergic responses and excessive inflammation. A nontoxic, biodegradable, biocompatible, self-adjuvanting vaccine delivery system is urgently needed. Herein, we report a potent vaccine delivery system fulfilling the above requirements. A peptide antigen was coupled with poly-hydrophobic amino acid sequences serving as self-adjuvanting moieties using solid-phase synthesis, to produce fully defined single molecular entities. Under aqueous conditions, these molecules self-assembled into distinct nanoparticles and chain-like aggregates. Following subcutaneous immunization in mice, these particles successfully induced opsonic epitope-specific antibodies without the need of external adjuvant. Mice immunized with entities bearing 15 leucine residues were able to clear bacterial load from target organs without triggering the release of soluble inflammatory mediators. Thus, we have developed a well-defined and effective self-adjuvanting delivery system for peptide antigens.


Subject(s)
Drug Delivery Systems , Inflammation/prevention & control , Vaccines, Subunit/pharmacology , Vaccines/pharmacology , Adjuvants, Immunologic/pharmacology , Amino Acids/chemistry , Amino Acids/immunology , Animals , Biocompatible Materials/chemistry , Biocompatible Materials/pharmacology , Epitopes/drug effects , Epitopes/immunology , Humans , Immunity, Mucosal/immunology , Inflammation/immunology , Mice , Nanoparticles/chemistry , Vaccines/chemistry , Vaccines/immunology , Vaccines, Subunit/chemistry , Vaccines, Subunit/immunology
12.
J Assist Reprod Genet ; 37(2): 369-384, 2020 Feb.
Article in English | MEDLINE | ID: mdl-31930433

ABSTRACT

PURPOSE: Chemical fixation is a critical step to retaining cellular targets as naturally as possible. Recent developments in microscopy allow sophisticated detection and measuring techniques with which spatio-temporal molecular alterations are conceivable. In this study, we compare two members of aldehyde fixatives [i.e., glyoxal (Gly) and paraformaldehyde (PFA)] to determine whether Gly, a less toxic dialdehyde fixative that is considered to retain immunoreactivity could provide a successful and consistent cell fixation in favor of PFA in various cell preparations and types. METHODS: We document the fixation competence of Gly and PFA side-by-side (with or without Triton X-100 permeabilization) in live- and fixed-cell preparations in mouse oocytes, embryos, and human somatic cells (human umbilical cord-derived mesenchymal stromal cells) using protein quantification by Western blot assay and super-resolution microscopy. RESULTS: Although Gly seemed to act faster than PFA, catastrophic consequences were found not acceptable, especially in oocytes and embryos. Due to cell lysate and immunocytochemistry surveys, it was obvious that PFA is superior to Gly in retaining cellular proteins in situ with little/no background staining. In many samples, PFA revealed more reliable and consistent results regarding the protein quantity and cellular localization corresponding to previously defined patterns in the literature. CONCLUSION: Although the use of Gly is beneficial as indicated by previous reports, we concluded that it does not meet the requirement for proper fixation, at least for the tested cell types and proteins. However, PFA alone with no addition of TX displayed a significant cytoplasmic loss by generating membrane blebs during fixation.


Subject(s)
Fixatives/pharmacology , Formaldehyde/pharmacology , Immunohistochemistry , Oocytes/drug effects , Polymers/pharmacology , Animals , Embryo, Mammalian/drug effects , Embryo, Mammalian/immunology , Epitopes/drug effects , Epitopes/immunology , Female , Glyoxal/pharmacology , Humans , Mice , Oocytes/growth & development , Oocytes/immunology , Stem Cells/drug effects , Stem Cells/immunology
13.
Anal Biochem ; 586: 113417, 2019 12 01.
Article in English | MEDLINE | ID: mdl-31505161

ABSTRACT

Inactivation of horseradish peroxidase by hydrogen peroxide (H2O2) treatment is a convenient alternative to stripping for sequential chemiluminescent western blotting (WB). However, little evidence exists on whether H2O2 treatment affects epitope recognition. Here we show that H2O2 treatment had a negligible effect for most of the tested antibodies, whereas it could also eliminate or enhance antibody binding. Thus, H2O2 treatment has unpredictable effects on epitope recognition. Moreover, we demonstrate potential steric hindrance from previously bound antibodies. Hence, it would be advantageous to pre-test the suitability of antibodies for H2O2-treated WB, and to optimize conditions to mitigate steric interference with re-probing.


Subject(s)
Blotting, Western , Epitopes/analysis , Epitopes/drug effects , Hydrogen Peroxide/pharmacology
14.
Nat Commun ; 10(1): 3017, 2019 07 09.
Article in English | MEDLINE | ID: mdl-31289267

ABSTRACT

Differences among hosts, resulting from genetic variation in the immune system or heterogeneity in drug treatment, can impact within-host pathogen evolution. Genetic association studies can potentially identify such interactions. However, extensive and correlated genetic population structure in hosts and pathogens presents a substantial risk of confounding analyses. Moreover, the multiple testing burden of interaction scanning can potentially limit power. We present a Bayesian approach for detecting host influences on pathogen evolution that exploits vast existing data sets of pathogen diversity to improve power and control for stratification. The approach models key processes, including recombination and selection, and identifies regions of the pathogen genome affected by host factors. Our simulations and empirical analysis of drug-induced selection on the HIV-1 genome show that the method recovers known associations and has superior precision-recall characteristics compared to other approaches. We build a high-resolution map of HLA-induced selection in the HIV-1 genome, identifying novel epitope-allele combinations.


Subject(s)
Evolution, Molecular , HIV-1/genetics , HLA Antigens/immunology , Host-Pathogen Interactions/genetics , Models, Genetic , Anti-HIV Agents/pharmacology , Anti-HIV Agents/therapeutic use , Bayes Theorem , Datasets as Topic , Epitopes/drug effects , Epitopes/genetics , Epitopes/immunology , Genome, Viral/drug effects , HIV Infections/drug therapy , HIV Infections/immunology , HIV Infections/virology , HIV-1/drug effects , HIV-1/immunology , Host-Pathogen Interactions/immunology , Humans , Recombination, Genetic/drug effects , Recombination, Genetic/immunology , Selection, Genetic/drug effects , Selection, Genetic/immunology
15.
J Pept Sci ; 25(9): e3203, 2019 Sep.
Article in English | MEDLINE | ID: mdl-31347248

ABSTRACT

Plasmodium falciparum is the most lethal species of malaria. In infected human red blood cells, P. falciparum digests hemoglobin as a nutrient source, liberating cytotoxic free heme in the process. Sequestration and subsequent conversion of this byproduct into hemozoin, an inert biocrystalline heme aggregate, plays a key role in parasite survival. Hemozoin has been a longstanding target of antimalarials such as chloroquine (CQ), which inhibit the biocrystallization of free heme. In this study, we explore heme-binding interactions with histidine-rich-protein 2 (HRP2), a known malarial biomarker and purported player in free heme sequestration. HRP2 is notoriously challenging to target due to its highly repetitious sequence and irregular secondary structure. We started with three protein-catalyzed capture agents (PCCs) developed against epitopes of HRP2, inclusive of heme-binding motifs, and explored their ability to inhibit heme:HRP2 complex formation. Cocktails of the individual PCCs exhibit an inhibitory potency similar to CQ, while a covalently linked structure built from two separate PCCs provided considerably increased inhibition relative to CQ. Epitope-targeted disruption of heme:HRP2 binding is a novel approach towards disrupting P. falciparum-related hemozoin formation.


Subject(s)
Epitopes/drug effects , Heme/antagonists & inhibitors , Peptides/pharmacology , Protozoan Proteins/antagonists & inhibitors , Amino Acid Sequence , Antigens, Protozoan/genetics , Epitopes/genetics , Heme/genetics , Humans , Molecular Conformation , Peptides/chemistry , Protozoan Proteins/genetics , Recombinant Proteins/genetics
16.
Cancer Res ; 79(13): 3372-3382, 2019 07 01.
Article in English | MEDLINE | ID: mdl-31064847

ABSTRACT

Acute myeloid leukemia (AML) is a high-risk disease with a poor prognosis, particularly in elderly patients. Because current AML treatment relies primarily on untargeted therapies with severe side effects that limit patient eligibility, identification of novel therapeutic AML targets is highly desired. We recently described AT1413, an antibody produced by donor B cells of a patient with AML cured after allogeneic hematopoietic stem cell transplantation. AT1413 binds CD43s, a unique sialylated epitope on CD43, which is weakly expressed on normal myeloid cells and overexpressed on AML cells. Because of its selectivity for AML cells, we considered CD43s as a target for a bispecific T-cell-engaging antibody (bTCE) and generated a bTCE by coupling AT1413 to two T-cell-targeting fragments using chemo-enzymatic linkage. In vitro, AT1413 bTCE efficiently induced T-cell-mediated cytotoxicity toward different AML cell lines and patient-derived AML blasts, whereas endothelial cells with low binding capacity for AT1413 remained unaffected. In the presence of AML cells, AT1413 bTCE induced upregulation of T-cell activation markers, cytokine release, and T-cell proliferation. AT1413 bTCE was also effective in vivo. Mice either coinjected with human peripheral blood mononuclear cells or engrafted with human hematopoietic stem cells [human immune system (HIS) mice] were inoculated with an AML cell line or patient-derived primary AML blasts. AT1413 bTCE treatment strongly inhibited tumor growth and, in HIS mice, had minimal effects on normal human hematopoietic cells. Taken together, our results indicate that CD43s is a promising target for T-cell-engaging antibodies and that AT1413 holds therapeutic potential in a bTCE-format. SIGNIFICANCE: These findings offer preclinical evidence for the therapeutic potential of a bTCE antibody that targets a sialylated epitope on CD43 in AML.


Subject(s)
Antibodies, Bispecific/pharmacology , Epitopes/immunology , Leukemia, Myeloid, Acute/drug therapy , Leukosialin/immunology , Lymphocyte Activation/immunology , N-Acetylneuraminic Acid/metabolism , T-Lymphocytes/immunology , Animals , Apoptosis , Cell Proliferation , Cytotoxicity, Immunologic , Endothelial Cells/drug effects , Endothelial Cells/immunology , Endothelial Cells/metabolism , Epitopes/drug effects , Epitopes/metabolism , Female , Humans , Leukemia, Myeloid, Acute/immunology , Leukemia, Myeloid, Acute/metabolism , Leukemia, Myeloid, Acute/pathology , Leukocytes, Mononuclear/drug effects , Leukocytes, Mononuclear/immunology , Leukocytes, Mononuclear/metabolism , Lymphocyte Activation/drug effects , Mice , Mice, Inbred NOD , Mice, SCID , Prognosis , T-Lymphocytes/drug effects , T-Lymphocytes/metabolism , Tumor Cells, Cultured , Xenograft Model Antitumor Assays
17.
ACS Appl Mater Interfaces ; 11(10): 9824-9831, 2019 Mar 13.
Article in English | MEDLINE | ID: mdl-30758939

ABSTRACT

We describe the preparation and characterization of synthetic antibodies based on molecularly imprinted polymer nanoparticles (MIP-NPs) for the recognition and binding of the highly conserved and specific peptide motif SWSNKS (3S), an epitope of the envelope glycoprotein 41 (gp41) of human immunodeficiency virus type 1 (HIV-1). This motif is implicated in the decline of CD4+ T cells and leads to the deterioration of the immune system during HIV infection. Therefore, the development of MIP-NPs that can target and block the 3S peptide to prevent subsequent cascade interactions directed toward the killing of CD4+ T cells is of prime importance. Because most antibodies recognize their protein antigen via a conformational or structured epitope (as opposed to a linear epitope commonly used for molecular imprinting), we employed protein molecular modeling to design our template epitope so that it mimics the three-dimensional structure fold of 3S in gp41. The resulting template peptide corresponds to a cyclic structure composed of CGSWSNKSC, with the 3S motif well orientated for imprinting. MIP-NPs with a size of 65 nm were obtained by solid-phase synthesis and were water-soluble. They were prepared by a judicious combination of multiple functional monomers affording hydrogen bonding, ionic, π-π, and hydrophobic interactions, conferring high affinity and selectivity toward both the cyclic peptide and the whole gp41 protein. These results suggest that our MIPs could potentially be used for blocking the function of the 3S motif on the virus.


Subject(s)
Antibodies/administration & dosage , HIV Infections/drug therapy , Molecular Imprinting , Nanoparticles/administration & dosage , Peptides/administration & dosage , Amino Acid Motifs/immunology , Antibodies/immunology , Antibody Formation/immunology , CD4-Positive T-Lymphocytes/drug effects , CD4-Positive T-Lymphocytes/immunology , Epitopes/drug effects , Epitopes/immunology , HIV Envelope Protein gp41/immunology , HIV Infections/pathology , HIV Infections/virology , HIV-1/drug effects , HIV-1/pathogenicity , Humans , Hydrogen Bonding , Nanoparticles/chemistry , Peptides/chemical synthesis , Peptides/chemistry , Polymers/administration & dosage , Polymers/chemical synthesis , Polymers/chemistry , Protein Conformation/drug effects , T-Lymphocytes/drug effects , T-Lymphocytes/virology
19.
Comput Biol Chem ; 78: 74-80, 2019 Feb.
Article in English | MEDLINE | ID: mdl-30500555

ABSTRACT

Typhoid fever is a multisystemic illness caused by Salmonella enterica serovars Typhi and is resistant to most antibiotics and drugs. The resistance is conferred through multidrug resistance (MDR) proteins, which efflux most antibiotics and other drugs. We predicted potential candidate B-cell and T-cell epitopes using bio- and immune-informatics tools in the 11 MDR proteins - EmrA, EmrB, EmrD, MdtA, MdtB, MdtC, MdtG, MdtH, MdtK, MdtL and TolC. The antigenic potential of the MDR proteins was calculated using VaxiJen server. The B-cell and T-cell epitopes of the MDR proteins were predicted using BCPred and ProPredI and ProPred respectively. The binding affinities of the predicted T-cell epitopes were estimated using T-epitope designer and MHCPred tools. 10, 7, 5, 12, 14, 21, 26, 3, 3 and 3 B-cell epitopes were identified in EmrA, EmrB, EmrD, TolC, MdtA, MdtB, MdtC, MdtG, MdtH and MdtL respectively. We predicted 9 T-cell epitopes - YVSRRAVQP (EmrA), FGVANAISI (EmrB), MVNSQVKQA and YQGGMVNSQ (TolC), WDRTNSHKL (MdtA), FLRNIPTAI (MdtB), YVEQLGVTG (MdtG), VKWMYAIEA (MdtH) and LAHTNTVTL (MdtL) capable of eliciting both humoral and adaptive immune responses. These T-cell epitopes specifically bind to HLA alleles - DRB1*0101 and DRB1*0401. This is the first report of epitope prediction in the MDR proteins of S. Typhi. Taken together, these results indicate the MDR proteins - EmrA, MdtA and TolC are the most suitable vaccine candidates for S. Typhi. The findings of our study on the MDR proteins prove to be useful in the development of peptide-based vaccine for the prevention and/or treatment of typhoid fever.


Subject(s)
ATP Binding Cassette Transporter, Subfamily B/analysis , Epitopes/chemistry , Salmonella typhi/chemistry , ATP Binding Cassette Transporter, Subfamily B/drug effects , ATP Binding Cassette Transporter, Subfamily B/immunology , Anti-Bacterial Agents/chemistry , Anti-Bacterial Agents/pharmacology , Epitopes/drug effects , Epitopes/immunology , Microbial Sensitivity Tests , Models, Molecular , Salmonella typhi/drug effects , Salmonella typhi/immunology
20.
Allergy ; 74(4): 780-787, 2019 04.
Article in English | MEDLINE | ID: mdl-30394551

ABSTRACT

BACKGROUND: The preventive effect of allergen immunotherapy (AIT) on allergy and asthma development is currently assessed using primary and secondary AIT approaches. Knowledge of the immunological effects of these interventions is limited and the impact on epitope diversity remains to be defined. METHODS: We used high-density peptide arrays that included all known Dermatophagoides pteronyssinus (Der p) and Dermatophagoides farinae (Der f) allergens and the whole proteome of Der f to study changes in House Dust Mite (HDM) linear peptide recognition during a 2-year preventive double-blind placebo-controlled sublingual HDM AIT pilot study in 2-5-year-old children with sensitization to HDM but without symptoms. RESULTS: Preventive AIT-treated patients showed significantly higher IgG epitope diversity to HDM allergens compared to placebo-treated individuals at 24 months of treatment (P < 0.05), while no increase in IgE diversity was seen. At 24 months of treatment, IgG4 diversity for HDM allergens was significantly higher in the pAIT-treated patients compared to placebo group (P < 0.05). Potentially beneficial changes in epitope recognition throughout the treatment are also seen in peptides derived from Der f proteome. CONCLUSION: These data suggest a beneficial immunomodulation of preventive sublingual immunotherapy at a molecular level by favoring a broader blocking repertoire and inhibiting epitope spreading.


Subject(s)
Epitopes/drug effects , Pyroglyphidae/immunology , Sublingual Immunotherapy/methods , Animals , Antigens, Dermatophagoides/immunology , Child, Preschool , Dermatophagoides pteronyssinus/immunology , Double-Blind Method , Female , Humans , Male , Pilot Projects
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