Steep Decline in Binding Capability of SARS-CoV-2 Omicron Variant (B.1.1.529) RBD to the Antibodies in Early COVID-19 Convalescent Sera and Inactivated Vaccine Sera.

A new SARS-CoV-2 variant B.1.1.529 was named by the WHO as Omicron and classified as a Variant of Concern (VOC) on 26 November 2021. Because this variant has more than 50 mutations, including 30 mutations on the spike, it has generated a lot of concerns on the potential impacts of the VOC on COVID-19. Here through ELISA assays using the recombinant RBD proteins with sequences the same to that of SARS-CoV-2 WIV04 (lineage B.1), the Delta variant and the Omicron variant as the coating antigens, the binding capabilities between the RBDs and the antibodies in COVID-19 convalescent sera and vaccine sera after two doses of the inactivated vaccine produced by Sinopharm WIBP are compared with each other. The results showed that the Omicron variant may evade antibodies induced by the ancestral strain and by the inactivated vaccine, with significant reduction in the binding capability of its RBD much greater than that of the Delta variant.

Harnessing Avidity: Quantifying the Entropic and Energetic Effects of Linker Length and Rigidity for Multivalent Binding of Antibodies to HIV-1.

IgG antibodies increase their apparent affinities by using both of their Fabs to simultaneously attach to antigens. HIV-1 foils this strategy by having few, and highly separated, Envelope (Env) spike targets for antibodies, forcing most IgGs to bind monovalently. Here, we develop a statistical mechanics model of synthetic diFabs joined by DNA linkers of different lengths and flexibilities. This framework enables us to translate the energetic and entropic effects of the linker into the neutralization potency of a diFab. We demonstrate that the strongest neutralization potencies are predicted to require a rigid linker that optimally spans the distance between two Fab binding sites on an Env trimer and that avidity can be further boosted by incorporating more Fabs into these constructs. These results inform the design of multivalent anti-HIV-1 therapeutics that utilize avidity effects to remain potent against HIV-1 in the face of the rapid mutation of Env spikes.

Attentive Cross-Modal Paratope Prediction.

Antibodies are a critical part of the immune system, having the function of recognizing and mediating the neutralization of undesirable molecules (antigens) for future destruction. Being able to predict which amino acids belong to the paratope , the region on the antibody that binds to the antigen, can facilitate antibody engineering and predictions of antibody-antigen structures. The suitability of deep neural networks has recently been confirmed for this task, with Parapred outperforming all prior models. In this work, we first significantly outperform the computational efficiency of Parapred by leveraging à trous convolutions and self-attention. Second, we implement cross-modal attention by allowing the antibody residues to attend over antigen residues. This leads to new state-of-the-art results in paratope prediction, along with novel opportunities to interpret the outcome of the prediction.

Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity.

The immune system has developed a number of distinct complex mechanisms to shape and control the antibody repertoire. One of these mechanisms, the affinity maturation process, works in an evolutionary-like fashion: after binding to a foreign molecule, the antibody-producing B-cells exhibit a high-frequency mutation rate in the genome region that codes for the antibody active site. Eventually, cells that produce antibodies with higher affinity for their cognate antigen are selected and clonally expanded. Here, we propose a new statistical approach based on maximum entropy modeling in which a scoring function related to the binding affinity of antibodies against a specific antigen is inferred from a sample of sequences of the immune repertoire of an individual. We use our inference strategy to infer a statistical model on a data set obtained by sequencing a fairly large portion of the immune repertoire of an HIV-1 infected patient. The Pearson correlation coefficient between our scoring function and the IC50 neutralization titer measured on 30 different antibodies of known sequence is as high as 0.77 (p-value 10-6), outperforming other sequence- and structure-based models.

Both binding and blocking antibodies correlate with disease severity in myasthenia gravis.

Myasthenia gravis (MG) is an autoimmune disease associated with antibodies directed to the postsynaptic muscle components of the neuromuscular junction. The heterogeneous nature of the acetylcholine receptor (AChR) antibody response had led to the categorization of AChR antibodies into 3 types: binding, blocking, and modulating antibodies. The purpose of this study is to compare the AChR antibodies' type with the clinical severity of MG patients. The patients enrolled in the study had been tested for both binding and blocking antibodies and had disease duration exceeding 2 years since diagnosis. The patients were divided into five main classes by the Myasthenia Gravis Foundation of America clinical classification. Again, the enrolled patients were divided into ocular and generalized group. We compared the type and titer of antibodies and the thymus status between the ocular and generalized group. Thirty-five patients met the inclusion criteria. Of these, 16 patients (47 %) had both blocking and binding AChR antibodies, 11 patients (31 %) had only binding antibodies, and 8 patients (22 %) had only blocking antibodies. By defined clinical classification, the ocular and generalized groups included 10 and 25 patients, respectively. Sixteen patients in the generalized group possessed both AChR antibodies, with the remaining patients displaying only the binding antibody. All the patients with only blocking antibody were classified into ocular group. Use of binding and blocking antibodies' tests may, therefore, be more helpful in predicting the prognosis and diagnoses of MG patient.

Key mutations stabilize antigen-binding conformation during affinity maturation of a broadly neutralizing influenza antibody lineage.

Affinity maturation, the process in which somatic hypermutation and positive selection generate antibodies with increasing affinity for an antigen, is pivotal in acquired humoral immunity. We have studied the mechanism of affinity gain in a human B-cell lineage in which two main maturation pathways, diverging from a common ancestor, lead to three mature antibodies that neutralize a broad range of H1 influenza viruses. Previous work showed that increased affinity in the mature antibodies derives primarily from stabilization of the CDR H3 loop in the antigen-binding conformation. We have now used molecular dynamics simulations and existing crystal structures to identify potentially key maturation mutations, and we have characterized their effects on the CDR H3 loop and on antigen binding using further simulations and experimental affinity measurements, respectively. In the two maturation pathways, different contacts between light and heavy chains stabilize the CDR H3 loop. As few as two single-site mutations in each pathway can confer substantial loop stability, but none of them confers experimentally detectable stability on its own. Our results support models of the germinal center reaction in which two or more mutations can occur without concomitant selection and show how divergent pathways have yielded functionally equivalent antibodies.

Cation-π, amino-π, π-π, and H-bond interactions stabilize antigen-antibody interfaces.

The identification of immunogenic regions on the surface of antigens, which are able to stimulate an immune response, is a major challenge for the design of new vaccines. Computational immunology aims at predicting such regions--in particular B-cell epitopes--but is far from being reliably applicable on a large scale. To gain understanding into the factors that contribute to the antigen-antibody affinity and specificity, we perform a detailed analysis of the amino acid composition and secondary structure of antigen and antibody surfaces, and of the interactions that stabilize the complexes, in comparison with the composition and interactions observed in other heterodimeric protein interfaces. We make a distinction between linear and conformational B-cell epitopes, according to whether they consist of successive residues along the polypeptide chain or not. The antigen-antibody interfaces were shown to differ from other protein-protein interfaces by their smaller size, their secondary structure with less helices and more loops, and the interactions that stabilize them: more H-bond, cation-π, amino-π, and π-π interactions, and less hydrophobic packing; linear and conformational epitopes can clearly be distinguished. Often, chains of successive interactions, called cation/amino-π and π-π chains, are formed. The amino acid composition differs significantly between the interfaces: antigen-antibody interfaces are less aliphatic and more charged, polar and aromatic than other heterodimeric protein interfaces. Moreover, paratopes and epitopes-albeit to a lesser extent-have amino acid compositions that are distinct from general protein surfaces. This specificity holds promise for improving B-cell epitope prediction.

Variable region identical immunoglobulins differing in isotype express different paratopes.

The finding that the antibody (Ab) constant (C) region can influence fine specificity suggests that isotype switching contributes to the generation of Ab diversity and idiotype restriction. Despite the centrality of this observation for diverse immunological effects such as vaccine responses, isotype-restricted antibody responses, and the origin of primary and secondary responses, the molecular mechanism(s) responsible for this phenomenon are not understood. In this study, we have taken a novel approach to the problem by probing the paratope with (15)N label peptide mimetics followed by NMR spectroscopy and fluorescence emission spectroscopy. Specifically, we have explored the hypothesis that the C region imposes conformational constraints on the variable (V) region to affect paratope structure in a V region identical IgG(1), IgG(2a), IgG(2b), and IgG(3) mAbs. The results reveal isotype-related differences in fluorescence emission spectroscopy and temperature-related differences in binding and cleavage of a peptide mimetic. We conclude that the C region can modify the V region structure to alter the Ab paratope, thus providing an explanation for how isotype can affect Ab specificity.

Induction of axon growth arrest without growth cone collapse through the N-terminal region of four-transmembrane glycoprotein M6a.

During development, axons elongate vigorously, carefully controlling their speed, to connect with their targets. In general, rapid axon growth is correlated with active growth cones driven by dynamic actin filaments. For example, when the actin-driven tip is collapsed by repulsive guidance molecules, axon growth is severely impaired. In this study, we report that axon growth can be suppressed, without destroying the actin-based structure or motility of the growth cones, when antibodies bind to the four-transmembrane glycoprotein M6a concentrated on the growth cone edge. Surprisingly, M6a-deficient axons grow actively but are not growth suppressed by the antibodies, arguing for an inductive action of the antibody. The binding of antibodies clusters and displaces M6a protein from the growth cone edge membrane, suggesting that the spatial rearrangement of this protein might underlie the unique growth cone behavior triggered by the antibodies. Molecular dissection of M6a suggested involvement for the N-terminal intracellular domain in this antibody-induced growth cone arrest.

Binding of CDR-derived peptides is mechanistically different from that of high-affinity parental antibodies.

We present data that reveal crucial differences between the binding mode of anti-gastrin17 (G17, pyroEGPWLEEEEEAYGWMDF-NH(2)) monoclonal antibodies (mAbs) and their CDR-derived synthetic binders (SBs) with G17. The mAbs recognize the N-terminal sequence of G17 (pyroEGPWL) with nanomolar affinity and high sequence selectivity. Molecular simulations suggest that G17 recognition is based primarily on a multitude of weak antibody-ligand interactions (H-bonding, van der Waals, etc.) inside a structurally well-defined cleft-like binding pocket. Relatively small structural changes (e.g. G-2 to A for G17) have a drastic impact on affinity, which is characteristic for antibody-like binding. In contrast, SBs recognize various sequences, including G17-unrelated targets with affinities of 1:1 complexes estimated in the 0.1-1.0 mM range. In most cases however, the G17/SB complex stoichiometries are not well-defined, giving rise to multimer aggregate formation with high apparent complex stabilities. Mutational studies on both G17 and SBs reveal the importance of positively charged (K/R) and aromatic residues (W/Y/F) for G17/SB complex formation. We propose that the synthetic binders use combinations of electrostatic, hydrophobic, and/or cation-π interactions in a variety of ways due to their intrinsic flexibility. This may also be the reason for their relatively low target specificity. We speculate that our findings are of general relevance, in showing that high-affinity mAbs do not necessarily provide the optimal basis for functional mimics design.

Kinetic analysis of a human chorionic gonadotropin-beta epitope-paratope interaction.

Kinetics of protein-protein or ligand-ligate interaction has predominantly been studied by optical spectroscopy (particularly fluorescence) and surface plasmon resonance biosensors. Almost all such studies are based on association kinetics between ligand-ligate and suffer from certain methodological and interpretational limitations. Therefore, kinetic analyses of dissociation data of such interactions become indispensable. In the present investigation, the radiolabeled human chorionic gonadotropin-beta ((125)IhCGbeta) was employed as a probe and nitrocellulose (NC) as a solid support to immobilize monoclonal antibody (MAb) G(1)G(10).1. The NC-G(1)G(10).1-(125)IhCGbeta complex (NC(com)) was prepared and the dissociation of radiolabeled hCGbeta was carried out in the presence of excess unlabeled ligate. From the experimental dissociation data under varying ionic strength, dissociation constants (k(- 1)), association constants (k(+1)) and affinity constants (k(a)) were calculated. The values obtained were utilized in exploring the amino acid residues constituting an epitopic region of hCGbeta involved in interaction with the complementary paratope on MAb G(1)G(10).1. Kinetic data of the present study supported our recently published findings [using single step-solid phase radioimmunoassay (SS-SPRIA)] that the core region of hCGbeta epitope consists of Arg (94,95) and Asp (99) while a Lys (104) and a His (106) are in proximity to the core epitopic region. Based on the results of present investigation, we conclude that dissociation kinetics coupled with SS-SPRIA unequivocally provides considerable insight into the study of ligand-ligate interactions and epitope analysis.

Examining the non-linear relationship between monoclonal antiphospholipid antibody sequence, structure and function.

In the antiphospholipid syndrome (APS), pathogenic antiphospholipid antibodies (aPL) that cause thrombosis or pregnancy morbidity are characterized by binding to anionic phospholipids (PL) and beta2-glycoprotein I (beta(2)GPI). Sequence analysis of human monoclonal aPL has shown that high affinity for these antigens is associated with the presence of three particular amino acids: arginine (Arg), asparagine and lysine in the complementarity determining regions (CDRs) of their heavy and light chains. In vitro expression systems have been used to create variants of the antibodies in which these amino acids have been altered. In general, removal of Arg residues reduces affinity for anionic PL and beta(2)GPI. Arg at different positions in the sequence, however, have different effects on binding affinity and effects on binding are not always mirrored by effects on pathogenicity. This review will focus upon the sequence motifs that have been found to distinguish pathogenic from non-pathogenic aPL, and whether these or other properties may help to identify distinct pathogenic subsets of aPL. In particular, we will focus on our recent work in which we are trying to develop a better understanding of the molecular mechanisms involved in activation of target cells by pathogenic aPL. These studies, together with molecular models of antigen/antibody complexes, help us to understand exactly how pathogenic antibodies interact with antigens. Ultimately, this understanding may aid the design of more powerful diagnostic/prognostic assays and targeted therapeutic agents to block the pathogenic effects of these antibodies.

Antibodies and immunohistochemistry in extracellular matrix research.

Immunohistochemistry is a powerful investigative tool that can provide researchers with important supplemental information to the routine morphological assessment of musculo-skeletal connective tissues in health and disease and also during tissue repair and regeneration. A wide variety of antibodies (both monoclonal and polyclonal) are now available from commercial and non-commercial sources that recognise the major structural and soluble components of cellular and extracellular matrix compartments. These include antibodies towards the major collagen and proteoglycan species and their metabolites, glycosaminoglycans, glycoproteins, enzymes, enzyme generated neo-epitopes, growth factors, cytokines and related signalling molecules. In addition, cell surface markers, cytoskeletal components and many other cytoplasmic and nuclear proteins, too numerous to mention, can also be detected. When allied with high resolution imaging modalities (e.g. confocal laser scanning microscopy) immunohistochemistry thus has the potential to reveal a wealth of macromolecular information about the complex three-dimensional composition and organisation of cellular and extracellular matrix compartments in many different connective tissue types. These technologies can also be used to quantify signal intensities and thereby facilitate numerical computation of image data.

IL-1beta epitope mapping using site-directed mutagenesis and hydrogen-deuterium exchange mass spectrometry analysis.

Hu007, a humanized IgG1 monoclonal antibody, binds and neutralizes human, cynomolgus, and rabbit IL-1beta but only weakly binds to mouse and rat IL-1beta. Biacore experiments demonstrated that Hu007 and the type-I IL-1 receptor competed for binding to IL-1beta. Increasing salt concentrations decrease the association rate with only moderate effects on the dissociation rate, suggesting that long-range electrostatics are critical for formation of the initial complex. To understand the ligand-binding specificity of Hu007, we have mapped the critical residues involved in the recognition of IL-1beta. Selected residues in cynomolgus IL-1beta were mutated to the corresponding residues in mouse IL-1beta, and the effects of the changes on binding were evaluated by surface plasmon resonance measurements using Biacore. Specifically, substitution of F150S decreased binding affinity by 100-fold, suggesting the importance of hydrophobic interactions in stabilizing the antibody/antigen complex. Substitution of three amino acids near the N- and C-terminal regions of cIL-1beta with those found in mouse IL-1beta (V3I/S5Q/F150S) decreased the binding affinity of Hu007 to IL-1beta by about 1000-fold. Conversely, mutating the corresponding residues in mouse IL-1beta to the human sequence resulted in an increase in binding affinity of about 1000-fold. Hydrogen-deuterium exchange/mass spectrometry analysis confirmed that these regions of IL-1beta were protected from exchange because of antibody binding. The results from this study demonstrate that Hu007 binds to a region located in the open end of the beta-barrel structure of IL-1beta and blocks binding of IL-1beta to its receptor.

Photo-activated affinity-site cross-linking of antibodies using tryptophan containing peptides.

Affinity-based conjugation methods for antibodies can produce defined and reproducible conjugates. This requires that the target antibody has an affinity site for the ligand and that the ligand has a reactive site. These requirements are critical for the conjugation of antibodies designed for diagnostic and therapeutic application. Our laboratory has discovered a novel affinity of antibodies for the amino acid tryptophan using an azido derivative of tryptophan. Here we show that tryptophan without the azido group can be photo-cross-linked to antibodies. Biotinylated tryptophan peptides are photolysed into monoclonal and polyclonal antibodies and such biotinylated antibodies are used in avidin-based ELISA. With the simple and gentle tryptophan-affinity photo-conjugation of peptides, antibodies can be conjugated with peptides to enhance their potency and expand their targeting range.

Modeling and simulations of the pharmacokinetics of fluorophore conjugated antibodies in tumor vicinity for the optimization of fluorescence-based optical imaging.

BACKGROUND AND OBJECTIVES: One of the methods to detect and localize tumors in tissue is to use fluorophore conjugated specific antibodies as tumor surface markers. The goals of this study are to understand and quantify the pharmacokinetics of fluorophore conjugated antibodies in the vicinity of a tumor. This study concludes another stage of the development of a non-invasive fluorescenated antibody-based technique for imaging and localization of tumors in vivo. STUDY DESIGN/MATERIALS AND METHODS: A mathematical model of the pharmacokinetics of fluorophore conjugated antibodies in the vicinity of a tumor was developed based on histological staining experiments. We present the model equations of concentrations of antibodies and free binding sites. We also present a powerful simulation tool that we developed to simulate the imaging process. We analyzed the model and studied the effects of various independent parameters on the imaging result. These parameters included initial volume of markers (injected volume), total number of binding sites, tumor size, binding and dissociation rate constants, and the diffusion coefficient. We present the relations needed between these parameters in order to optimize the imaging results. RESULTS AND CONCLUSIONS: A powerful and accurate tool was developed which may assist in optimizing the imaging system results by setting the injection volume and concentration of fluorophore conjugated antibodies in tissue and approximating the time interval where maximum specific binding occurs and the tumor can be imaged.

Antibody-bound beta-amyloid precursor protein stimulates the production of tumor necrosis factor-alpha and monocyte chemoattractant protein-1 by cortical neurons.

Alzheimer's disease (AD) is an age-related neurodegenerative disorder characterized by the accumulation of extracellular depositions of fibrillar beta-amyloid (A beta), which is derived from the alternative processing of beta-amyloid precursor protein (APP). Although APP is thought to function as a cell surface receptor, its mode of action still remains elusive. In this study, we found that the culture medium derived from cortical neurons treated with an anti-APP antibody triggers the death of naive neurons. Biochemical and immunocytochemical analyses revealed the presence, both in the conditioned medium and in neurons, of increased levels of tumor necrosis factor-alpha and monocyte chemoattractant protein-1. Furthermore, the expression of these proinflammatory mediators occurred through a c-Jun N-terminal protein kinase/c-Jun-dependent mechanism. Taken together, our findings provide evidence for a novel mechanism whereby neuronal APP in its full-length configuration induces neuronal death. Such a mechanism might be relevant to neuroinflammatory processes as those observed in AD.

Cross-reactivity of mimotopes with a monoclonal antibody against the high molecular weight melanoma-associated antigen (HMW-MAA) does not predict cross-reactive immunogenicity.

The high molecular weight melanoma-associated antigen (HMW-MAA) is highly expressed in advanced primary and metastatic melanoma. An epitope of the core protein of HMW-MAA is recognized by the murine monoclonal antibody (mAb) 225.28S. In this study, we aimed to characterize peptides that antigenically mimicked this epitope and to determine their efficacy as components of an HMW-MAA-based anti-melanoma vaccine. Therefore, we screened a constrained 10 mer phage display peptide library against mAb 225.28S. Selected phage-displayed peptides were then tested for their specificity for the antibody's antigen-binding site. DNA sequences coding for specific peptide ligands were determined. Binding of mAb 225.28S to HMW-MAA was inhibited in a dose-dependent manner by phage-displayed peptides from 51 to 83% and by synthetic peptides from 38 to 87%. Subsequently, the immunogenicity of the five mimotopes with the highest inhibition capacity was examined in rabbits. Immunizations with synthetic mimotopes conjugated to tetanus toxoid resulted in peptide-specific antibodies, but none of the highly antigenic mimotopes induced HMW-MAA cross-reactive antibodies. This report describes an example of disparity between antigenicity and cross-reactive immunogenicity, complicating the selection of potential vaccine candidates.

Irreversible engineering of the multielement-binding antibody 2D12.5 and its complementary ligands.

Engineering the permanent formation of a receptor-ligand complex has a number of potential applications in chemistry and biology, including targeted medical imaging and therapy. Starting from the crystal structure of the rare-earth-DOTA binding antibody 2D12.5 (Corneillie, T. M., Fisher, A. J., and Meares, C. F. (2003) J. Am. Chem. Soc. 125, 15039-15048), we used the site-directed incorporation of cysteine nucleophiles at the periphery of the antibody's binding site, paired with the chemical design of a weakly electrophilic ligand, to produce a receptor-ligand pair that associates efficiently and permanently. Protein residues proximal to the ligand's side chain were identified for engineering cysteine mutants. Fab fragments incorporating a cysteine at position 54, 55, or 56 of the heavy chain (complementarity determining region 2) were designed from the structure and then cloned, expressed in Drosophila S2 cells, and tested for reactivity with mildly electrophilic DOTA-yttrium ligands. All showed permanent binding activity, indicating that there is some tolerance for the location of the reactive mutant on the protein surface near the binding site. The G54C Fab mutant displayed the highest expression levels and permanent binding activity in initial experiments and was produced in high yield for further study. Upon examining the behavior of the G54C mutant with a small set of electrophilic ligands, differences in reactivity were observed which indicated that the substituents near the electrophilic atom can be important determinants of permanent binding. The G54C mutant permanently attaches to Y(3+) complexes of (S)-2-(4-acrylamidobenzyl)-DOTA with a half-time of approximately 13 min at 37 degrees C, making it potentially useful for in vivo pretargeting applications.