Antibody Therapeutics

BackgroundSialyl Lewis A (sLeA), or the CA 19-9 marker, is a tetrasaccharide and a tumour-associated carbohydrate antigen (TACA) overexpressed and abnormally secreted as a serum-borne marker in gastrointestinal malignancies. CA 19-9 is the best validated and only FDA-approved serologic marker clinically used to monitor recurrence, progression, and therapy efficiency in pancreatic ductal adenocarcinoma (PDAC) patients. Due to its altered expression on cancer cells, sLeA is also an attractive target for antibody development. Although recent clinical trials have demonstrated insufficient efficacy of the fully human anti-sLeA 5B1 (MVT-5873) format as a stand-alone drug or an adjuvant therapy in PDAC [1], its safety profile and unique expression in additional malignancies keep CA 19-9 an attractive TACA. Hence, we set out to explore the use of synthetic sLeA to develop novel monoclonal antibodies (mAbs) with improved sLeA recognition and better efficacy. MethodsTwo mAbs targeting sLeA were generated through mice immunisation with synthetic sLeA glycoconjugates, synthetic glycan arrays, and hybridoma technology. We then compared the antigen-binding properties of the newly developed mAbs with the widely used mAb 1116-NS-19- 9 via synthetic glycan arrays, immunohistochemistry (IHC), X-ray crystallography, molecular dynamics (MD) simulation, and Saturation Transfer Difference Nuclear Magnetic Resonance (STD NMR) spectroscopy. ResultsThe newly generated mAbs demonstrated improved affinity and specificity for both synthetic and native sLeA, surpassing the performance of the established mAb 1116-NS-19-9. First, synthetic glycan arrays, surface plasmon resonance (SPR), and isothermal titration calorimetry (ITC) assays confirmed superior antigen-binding properties to synthetic sLeA. In particular, the mAb designated GB11 demonstrated markedly enhanced binding to native sLeA ectopically expressed in B16 melanoma cells. To elucidate the structural origin of GB11s improved antigen binding, we conducted high-resolution mapping of the molecular recognition patterns between sLeA and the different antibodies using X-ray crystallography and STD NMR. These analyses revealed subtle yet critical differences in the glycan engagement and identified key structural features underlying GB11s enhanced recognition of sLeA. MD simulations further supported these observations, indicating distinct orientations of sLeA within the binding pockets of each mAb. ConclusionOur results suggest better recognition of the sLeA antigen by the newly generated GB11 antibody and provide a detailed high-resolution elucidation of the molecular interactions behind it. Our study may provide a novel tool with improved theranostic properties against sLeA-overexpressing malignancies.

Bispecific T cell engager (TCE) is an emerging anti-cancer modality which redirects cytotoxic T cells to tumor cells expressing tumor-associated antigen (TAA) thereby forming immune synapses to exerts anti-tumor effects. Considering the protein engineering challenges in designing and optimizing size and pharmacokinetically acceptable TCEs in the context of the complexity of intercellular bridging between T cells and tumor cells, a physiologically relevant and clinically verified computational modeling framework is of crucial importance to guide the process to understand the protein engineering trade offs. In this study, we developed a quantitative, physiologically based computational framework to predict immune synapse formation for a variety of molecular format of TCEs in tumor tissue. Our model incorporated the molecular size dependent biodistribution using the two pore theory, extra-vascularization of T cells and hematologic cancer cells, mechanistic bispecific intercellular binding of TCEs and competitive inhibitory interaction by shed targets. The biodistribution of TCE was verified by positron emission tomography imaging of [89Zr]AMG211 (a carcinoembryonic antigen-targeting TCE) in patients. Parameter sensitivity analyses indicated that immune synapse formation was highly sensitive to TAA expression, degree of target shedding and binding selectivity to tumor cell surface TAA over shed target. Interestingly, the model suggested a "sweet spot" for TCEs CD3 binding affinity which balanced the trapping of TCE in T cell rich organs. The final model simulations indicated that the number of immune synapses is similar ([~]50/tumor cell) between two distinct clinical stage B cell maturation antigen (BCMA)-targeting TCEs, PF-06863135 in IgG format and AMG420 in BiTE format, at their respective efficacious dose in multiple myeloma patients, demonstrating the applicability of the developed computational modeling framework to molecular design optimization and clinical benchmarking for TCEs. This framework can be employed to other targets to provide a quantitative means to facilitate the model-informed best in class TCE discovery and development. Author summaryCytotoxic T cells play a crucial role in eliminating tumor cells. However, tumor cells develop mechanisms to evade from T cell recognition. Bispecific T cell engager (TCE) is designed to overcome this issue with bringing T cells to close proximity of tumor cells through simultaneous bivalent binding to both tumor-associated antigen and T cells. After successful regulatory approval of blinatumomab (anti-CD19 TCE), more than 40 TCEs are currently in clinical development with a variety of molecular size and protein formats. In this study, we developed a quantitative computational modeling framework for molecular design optimization and clinical benchmarking of TCEs. The model accounts for molecular size dependent biodistribution of TCEs to tumor tissue and other organs as well as following bispecific intercellular bridging of T cells and tumor cells. The model simulation highlighted the importance of binding selectivity of TCEs to tumor cell surface target over shed target. The model also demonstrated a good agreement in predicted immune synapse number for two distinct molecular formats of TCEs at their respective clinically efficacious dose levels, highlighting the usefulness of developed computational modeling framework for best in class TCE discovery and development.

Preclinical evidence has suggested that the Glucocorticoid-Induced TNFR-related protein (GITR) may be valuable a target for the development of anticancer therapeutics, but clinical studies with GITR ligand (GITRL) have been disappointing. Here, we report the development of a fusion protein featuring GITR ligand (GITRL) fused to the F8 antibody which targets the alternatively-spliced EDA domain of fibronectin, a tumor-associated antigen often found around the tumor neovasculature. Five different formats for F8-GITRL fusion proteins were cloned and characterized, but quantitative biodistribution studies failed to evidence a preferential accumulation at the tumor site. The in vivo tumor targeting properties of F8-GITRL could be substantially improved by enzymatic deglycosylation or site-directed mutagenesis of the N-glycosylation consensus sequence. However, therapy studies in a murine model of cancer with the glycoengineered F8-GITRL N74S and N157T variant failed to elicit a durable anti-tumor response, both in monotherapy and in combination with PD-1 blockade. HIGHLIGHTSO_LIDifferent formats of fusion proteins featuring Glucocorticoid-induced TNFR-related protein ligand (GITRL) fused to a tumor-targeting antibody were produced. C_LIO_LIThe tumor uptake of the fusion proteins could be increased by enzymatic deglycosylation of the fusion protein or by site-directed mutagenesis of the N-glycosylation consensus sequences. C_LIO_LIThe fusion protein developed in this study failed to show any anti-tumor activity either alone or in combination with PD-1 inhibition. C_LI

Antibody based therapeutics targeting mesothelin (MSLN) have shown limited anticancer activity in clinical trials. Novel antibodies with high affinity and better therapeutic properties are needed. In the current study, we have isolated and characterized a novel VH domain 3C9 from a large size human immunoglobulin heavy chain variable (VH) domain library. 3C9 exhibited high affinity [KD (dissociation constant) < 3 nM] and binding specificity in a membrane proteome array (MPA). In a mouse xenograft model, 3C9 fused to human Fc became visible at tumor sites as early as 8 hours post infusion and persisted at the tumor site for more than 10 days. Both CAR-T cells and antibody domain drug conjugations (DDCs) generated with 3C9 were highly effective at killing MSLN positive cells in vitro without off-target effects. The X-ray crystal structure of full-length MSLN in complex with 3C9 reveals interaction of the 3C9 domains with two distinctive residues patches on the MSLN surface. 3C9 fused to human Fc domain drug conjugate was efficacious to inhibit tumor growth in a mouse xenograft model. This newly discovered VH antibody domain holds promise as a therapeutic candidate for MSLN-expressing cancers.

Defining the binding epitopes of antibodies is essential for understanding how they bind to their antigens and perform their molecular functions. However, while determining linear epitopes of monoclonal antibodies can be accomplished utilizing well-established empirical procedures, these approaches are generally labor- and time-intensive and costly. To take advantage of the recent advances in protein structure prediction algorithms available to the scientific community, we developed a calculation pipeline based on the localColabFold implementation of AlphaFold2 that can predict linear antibody epitopes by predicting the structure of the complex between antibody heavy and light chains and target peptide sequences derived from antigens. We found that this AlphaFold2 pipeline, which we call PAbFold, was able to accurately flag known epitope sequences for several well-known antibody targets (HA / Myc) when the target sequence was broken into small overlapping linear peptides and antibody complementarity determining regions (CDRs) were grafted onto several different antibody framework regions in the single-chain antibody fragment (scFv) format. To determine if this pipeline was able to identify the epitope of a novel antibody with no structural information publicly available, we determined the epitope of a novel anti-SARS-CoV-2 nucleocapsid targeted antibody using our method and then experimentally validated our computational results using peptide competition ELISA assays. These results indicate that the AlphaFold2-based PAbFold pipeline we developed is capable of accurately identifying linear antibody epitopes in a short time using just antibody and target protein sequences. This emergent capability of the method is sensitive to methodological details such as peptide length, AlphaFold2 neural network versions, and multiple-sequence alignment database. PAbFold is available at https://github.com/jbderoo/PAbFold.

BackgroundIMV-M is a MUC16xDR5 bispecific antibody has demonstrated MUC16-selective anti-tumor activity. However, it remained unclear whether multiple binding of IMV-M on a single MUC16 molecule was required for IMV-M cytotoxicity, whether circulating CA125 could attenuate its efficacy or cause off-target toxicity, and whether anti-drug antibodies might induce IMV-M aggregation and related adverse effects. MethodsA comparative analysis of three bispecific antibodies, IMV-M (sofituzumabxDR5), 11D10xDR5, and fluorxDR5, sharing an identical IgG1-anti-DR5 scFv architecture, was performed. Sofituzumab binds to multiple epitopes on a single MUC16 molecule, whereas 11D10 binds a single MUC16 epitope, and fluor does not bind any human antigen. Antibody binding to shed and cell-surface MUC16 was evaluated by ELISA and flow cytometry. Cytotoxicity was assessed in a MUC16+/DR5+ tumor cell line and MUC16-/DR5+ hepatic cell lines. Additional studies examined the effects of soluble CA125 and Fc-directed polyclonal antibodies on IMV-M activity. ResultsIMV-M bound MUC16 to a markedly higher extent than the 11D10xDR5 comparator, consistent with its multivalent engagement, while binding of fluorxDR5 to MUC16 was negligent. Only IMV-M induced potent cytotoxicity in MUC16+ tumor cells, whereas 11D10xDR5 and fluorxDR5 control antibodies were inactive, demonstrating that multivalent clustering on MUC16 is required for apoptosis. IMV-M showed no significant cytotoxicity toward hepatic cell lines, even in the presence of Fc-directed polyclonal antibodies or clinically relevant concentrations of soluble CA125. ConclusionsThese findings indicate that IMV-M cytotoxic activity requires clustering on MUC16, that CA125 at clinically relevant concentrations does not mediate IMV-M neutralization, and that aggregate formation with secondary antibodies or soluble MUC16 does not induce off-target toxicity.

Glycosylation of antibody plays an important role in Fc-mediated killing of tumor cells and virus-infected cells through effector functions such as antibody-dependent cellular cytotoxicity (ADCC), antibody dependent cell-mediated phagocytosis (ADCP) and vaccinal effect. Previous studies showed that therapeutical humanized antibodies with 2-6 sialyl complex type (SCT) glycan attached to Fc-Asn297 exhibited optimal binding to the Fc receptors on effector cells associated with ADCC, ADCP and vaccinal effect. However, the production of antibodies with homogeneous Fc-SCT needs multiple in vitro enzymatic and purification steps. In this study, we report two different approaches to shorten the processes to produce SCT-enriched antibodies. First, we expressed a bacterial endoglycosidase in GNT1-KO EXPI293 cells to trim all N-glycans to mono-GlcNAc glycoforms for in vitro transglycosylation to generate homogeneous SCT antibody. Second, we engineered the glycosylation pathway of HEK293 cells through knockout of the undesired glycosyltransferases and expression of the desired glycosyltransferases to produce SCT enriched antibodies with similar binding affinity to Fc receptors and ADCC activity to homogenous SCT antibody.

BackgroundMET overexpression is associated with poor prognosis in many solid tumors due to its central role in tumor survival, invasion, metastasis, and chemoresistance. While targeting MET with antibody-drug conjugates has shown promising results, engineered cellular immunotherapeutic approaches have not been extensively explored. Compared to conventional single-chain variable fragments (scFv), naturally occurring single-domain antibodies consisting of variable heavy chains only (VHH or nanobodies) are smaller, retain high specificity, and exhibit remarkable biochemical stability. In this study, we tested the efficacy of MET-targeting VHH-CAR-T (chimeric antigen receptor T cells). MethodsWe generated a panel of VHH-CAR-Ts using mRNA electroporation. VHH-CAR-T cells were evaluated in functional assays including cell binding avidity, cytokine production profiles, hydrogel microwell-based cellular kinetics, and in vitro cytotoxicity. We also assessed the therapeutic efficacy of VHH-CAR-T in an in vivo mouse model of metastatic triple negative breast cancer (TNBC). ResultsAmong the tested VHH, we identified those with intermediate avidity as most effective for in vitro tumor killing. VHH-CAR-Ts with CD28 costimulatory domains demonstrated augmented cytotoxicity with favorable selectivity, requiring a minimum antigen density threshold for activation. Mechanistically, VHH-CAR-Ts demonstrated low tonic signaling, high avidity, potent cytokine production, and rapid tumor killing kinetics. When administered in an mRNA format, VHH-CAR-Ts exhibited potent and prolonged control of tumor growth in an in vivo metastatic model of TNBC. ConclusionTaken together, these results demonstrate that VHH-CAR-Ts exhibit robust MET specificity and potent therapeutic efficacy both in vitro and in vivo. Thus, VHH-CAR-T cell therapy represents a promising immunotherapeutic strategy for targeting MET-overexpressing solid tumors. What is already known on this topicMET signaling is an important contributor to the aggressiveness of many solid tumors, and targeting MET by antibody-drug conjugates has shown efficacy and safety. Targeting MET by CAR-T cells has been under study, though with limited potency. What this study addsThis study is the first to demonstrate effectiveness of anti-MET VHH-CAR-T cells. Compared with other antigen binding domains, VHH-incorporated CAR-T cells show low tonic signaling, a favorable cytokine profile, and potent tumor killing. How this study might affect research, practice or policyWith the multiple advantages of VHHs including small size, stability, and low potential for tonic signaling, VHH-CAR-T cells represent a promising approach for CAR-T design against solid tumors.

Antibody humanization is an essential part of converting animal-derived antibodies into clinical candidates however conventional CDR grafting techniques often faces challenges, especially when essential antigen-binding sites extend beyond CDR regions. Additionally, the CDR grafting process tends to retain undesired non-human elements within the CDR regions. In this study, we overcame these challenges by using our proprietary AI-predicted antigen-antibody complex algorithm to effectively humanize a murine antibody. During our AI-powered humanization process, in contrast to traditional CDR grafting techniques, only the crucial paratopes identified through our AI-predicted complex structure were precision grafted onto a select human germline. This paratope grafting technique significantly reduced the antibodies immunogenicity risk while maintaining bioactivity. Moreover, all AI-guided deep humanized antibody variants demonstrated favorable developability, including thermal stability, poly-reactivity, and hydrophobicity. These results not only advance antibody humanization techniques but also demonstrate the power of AI in expediting antibody engineering and derisking clinical research.

BackgroundChimeric antigen receptor (CAR) technology has revolutionized the treatment of B-cell malignancies and steady progress is being made towards CAR-immunotherapies for solid tumours. Epidermal growth factor family receptors EGFR or HER2 are commonly overexpressed in cancer and represent proven targets for CAR-T therapy; given their expression in healthy tissues it is imperative that any targeting strategy consider the potential for on-target off-tumour toxicity. MethodsHerein, we utilize high-throughput CAR screening to identify novel camelid single-domain antibody CARs (sdCARs) with high EGFR-specific CAR-T response. To optimize antigenic sensitivity of this EGFR-sdCAR, we performed progressive N-terminal truncation of the human CD8 hinge domain used as a spacer in many CAR constructs. Hinge truncation resulted in decreased CAR sensitivity to EGFR and improved selectivity for EGFR-overexpressing cells over EGFR-low target cells or healthy donor derived EGFR-positive fibroblasts. To investigate the molecular mechanism of hinge truncation, we test hinge-truncated scFv-based CARs targeting membrane proximal or membrane distal domains of EGFR-family proteins, HER2 and EGFRvIII. Finally, we proceed to test hinge variant EGFR-sdCAR functionality through in vitro and in vivo assessments in primary T cells derived from multiple donors. ResultsFor CARs targeting membrane-proximal epitopes, hinge truncation by even a single amino acid provided fine control of the antigenic sensitivity, whereas CARs targeting membrane distal domains were not sensitive to even complete hinge domain removal. Hinge-modified EGFR-sdCARs showed consistent and predictable responses in Jurkat-CAR cells and primary human CAR-T cells in vitro and in vivo. ConclusionsOverall, these results indicate that membrane-proximal epitope targeting CARs can be modified through hinge length tuning for programmable antigenic sensitivity and improved tumour selectivity. O_FIG O_LINKSMALLFIG WIDTH=196 HEIGHT=200 SRC="FIGDIR/small/360925v2_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@1f0db64org.highwire.dtl.DTLVardef@1d3ac43org.highwire.dtl.DTLVardef@1d270faorg.highwire.dtl.DTLVardef@f7614f_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LISingle amino acid truncations of CD8-hinge domain provide precise control of CAR antigen sensitivity C_LIO_LITruncated hinge CARs show enhanced selectivity for antigen overexpressing tumour cells and decreased activity towards healthy antigen-expressing cells C_LIO_LIEpitope location is a critical factor in determining hinge sensitivity for a CAR C_LIO_LIHinge tuning can modulate CAR-T antigenic sensivity in vitro and in vivo C_LI

Glycosylation on therapeutic antibodies is critically important for their drug efficacies. Here, using NISTmAb and Humira(R) as examples, we present methods of glycan fingerprinting for these antibodies. Glycans are first released with PNGase F or Endo S2, and then labeled by specific glycosyltransferases, including sialyltransferase ST6Gal1, fucosyltransferase FUT9, N-acetyl-glucosaminyltransferase MGAT3 and fucosyltransferase FUT8, with respective fluorophore-conjugated donor sugars. The labeled glycans are then separated by gel electrophoresis (SDS-PAGE). A fluorophore-labeled hyaluronan ladder is run along with the samples to reveal the relative mobility of each glycan band. Pretreatment of the samples with specific glycosidase or glycosyltransferase results in additional mobility shift of specific glycan bands, which allows identification of some of these bands. Particularly, we report the identification of -Gal epitopes, core-6 fucosylated glycans, paucimannose glycans and likely some bisecting/tri-antennary glycans on NISTmAb. Overall, our methods could serve as quick assessments of glycosylation on therapeutic antibodies.

B cells specific for the SARS-CoV-2 S envelope glycoprotein spike were isolated from a COVID-19-infected subject using a stabilized spike-derived ectodomain (S2P) twenty-one days post-infection. Forty-four S2P-specific monoclonal antibodies were generated, three of which bound to the receptor binding domain (RBD). The antibodies were minimally mutated from germline and were derived from different B cell lineages. Only two antibodies displayed neutralizing activity against SARS-CoV-2 pseudo-virus. The most potent antibody bound the RBD in a manner that prevented binding to the ACE2 receptor, while the other bound outside the RBD. Our study indicates that the majority of antibodies against the viral envelope spike that were generated during the first weeks of COVID-19 infection are non-neutralizing and target epitopes outside the RBD. Antibodies that disrupt the SARS-CoV-2 spike-ACE2 interaction can potently neutralize the virus without undergoing extensive maturation. Such antibodies have potential preventive/therapeutic potential and can serve as templates for vaccine-design. IN BRIEFSARS-CoV-2 infection leads to expansion of diverse B cells clones against the viral spike glycoprotein (S). The antibodies bind S with high affinity despite being minimally mutated. Thus, the development of neutralizing antibody responses by vaccination will require the activation of certain naive B cells without requiring extensive somatic mutation. HighlightsO_LIAnalysis of early B cell response to SARS-CoV-2 spike protein C_LIO_LIMost antibodies target non-neutralizing epitopes C_LIO_LIPotent neutralizing mAb blocks the interaction of the S protein with ACE2 C_LIO_LINeutralizing antibodies are minimally mutated C_LI

The emergence of highly immune invasive and transmissible variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has decreased the effectiveness of existing vaccines. It is, therefore, critical to develop effective and safe therapeutics for SARS-CoV-2 infections, especially for the most vulnerable and immunocompromised patients. Neutralizing antibodies have been shown to be successful at preventing severe disease from early SARS-CoV-2 strains, although their efficacy has diminished with the emergence of new variants. Here, we aim to develop fully human and broadly neutralizing monoclonal (mAb) and bispecific (BsAb) antibodies against SARS-CoV-2 and its variants. Specifically, we first identified two antibodies from human transgenic mice that bind to the receptor binding domain (RBD) of the SARS-CoV-2 spike protein and are capable of neutralizing SARS-CoV-2 and variants of concern with high to moderate affinity. Two non-competing clones with the highest affinity and functional blocking of ACE2 binding were then selected to be engineered into two BsAbs, which were then demonstrated to have relatively improved affinity, ACE2 blocking ability, and pseudovirus inhibition against several variants, including Omicron (B.1.1.529). Our findings provide one mAb candidate and two bsAb candidates for consideration of further clinical development and suggest that the bispecific format may be more effective than mAbs for SARS-CoV-2 treatment.

SARS-CoV-2 virus has continued to evolve over time necessitating the adaptation of vaccines to maintain efficacy. Monoclonal antibodies (mAbs) against SARS-CoV-2 were a key line of defense for unvaccinated or immunocompromised individuals. However, these mAbs are now ineffective against current SARS-CoV-2 variants. Here, we tested three aspects of SARS-CoV-2 therapeutics. First, we tested whether Fc engagement is necessary for in vivo clearance of SARS-CoV-2. Secondly, we tested bi-specific killer engagers (BiKEs) that simultaneously engage SARS-CoV-2 and a specific Fc receptor. Benefits of these engagers include the ease of manufacturing, stability, more cell-specific targeting, and high affinity binding to Fc receptors. Using both mAbs and BiKEs, we found that both neutralization and Fc receptor engagement were necessary for effective SARS-CoV-2 clearance. Thirdly, due to ACE2 being necessary for viral entry, ACE2 will maintain binding to SARS-CoV-2 despite viral evolution. Therefore, we used an ACE2 decoy Fc-fusion or BiKE, instead of an anti-SARS-CoV-2 antibody sequence, as a potential therapeutic that would withstand viral evolution. We found that the ACE2 decoy approach also required Fc receptor engagement and, unlike traditional neutralizing antibodies against specific variants, enabled the clearance of two distinct SARS-CoV-2 variants. These data show the importance of Fc engagement for mAbs, the utility of BiKEs as therapies for infectious disease, and the in vivo effectiveness of the ACE2 decoy approach. With further studies, we predict combining neutralization, the cellular response, and this ACE2 decoy approach will benefit individuals with ineffective antibody levels. AbbreviationsACE2, scFv, mAb, BiKE, COVID-19, Fc, CD16, CD32b, CD64, d.p.i Key pointsO_LIWith equal dosing, both neutralization and Fc engagement are necessary for the optimal efficacy of in vivo antibodies and bi-specific killer engagers (BiKEs) against SARS-CoV-2. C_LIO_LIBiKEs can clear SARS-CoV-2 virus and protect against severe infection in the hACE2-K18 mouse model. C_LIO_LIACE2 decoys as part of Fc-fusions or BiKEs provide in vivo clearance of two disparate SARS-CoV-2 variants. C_LI

The Coronavirus disease 2019 (COVID19) pandemic caused by Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) is an ongoing threat to global public health. To this end, intense efforts are underway to develop reagents to aid in diagnostics, enhance preventative measures, and provide therapeutics for managing COVID-19. The recent emergence of SARS-CoV-2 Omicron variants with enhanced transmissibility, altered antigenicity, and significant escape of existing monoclonal antibodies and vaccines underlines the importance of the continued development of such agents. The SARS-CoV-2 spike protein and its receptor binding domain (RBD) are critical to viral attachment and host cell entry and are primary targets for antibodies elicited from both vaccination and natural infection. In this study, mice were immunized with two synthetic peptides (Pep 1 and Pep 2) within the RBD of the original Wuhan SARS-CoV-2, as well as the whole RBD as a recombinant protein (rRBD). Hybridomas were generated and a panel of three monoclonal antibodies, mAb CU-P1-1 against Pep 1, mAb CU-P2-20 against Pep 2, and mAb CU-28-24 against rRBD, were generated and further characterized. These mAbs were shown by ELISA to be specific for each immunogen/antigen. Monoclonal antibody CU-P1-1 has limited applicability other than in ELISA approaches and basic immunoblotting. Monoclonal antibody CU-P2-20 is shown to be favorable for ELISA, immunoblotting, and immunohistochemistry (IHC), however, not live virus neutralization. In contrast, mAb CU-28-24 is most effective at live virus neutralization as well as ELISA and IHC. Moreover, mAb CU-28-24 was active against rRBD proteins from Omicron variants B.2 and B.4/B5 as determined by ELISA, suggesting this mAb may neutralize live virus of these variants. Each of the immunoglobulin genes has been sequenced using Next Generation Sequencing, which allows the expression of respective recombinant proteins, thereby eliminating the need for long-term hybridoma maintenance. The synthetic peptides and hybridomas/mAbs are under the intellectual property management of the Clemson University Research Foundation, and the three CDRs have been submitted as an invention disclosure for further patenting and commercialization.

With the rapid spread of SARS-CoV-2 variants, including those that are resistant to antibodies authorized for emergency use, it is apparent that new antibodies may be needed to effectively protect patients against more severe disease. Differences between the murine and human antibody repertoires may allow for the isolation of murine monoclonal antibodies that recognize a different or broader range of SARS-CoV-2 variants than the human antibodies that have been characterized so far. We describe mouse antibodies B13 and O24 that demonstrate neutralizing potency against SARS-CoV-2 Wuhan (D614G) and B.1.351 variants. Such murine antibodies may have advantages in protecting against severe symptoms when individuals are exposed to new SARS-CoV-2 variants.

Assays for cancer diagnosis via the analysis of tumor biomarkers on circulating extracellular vesicles (EVs) have shown great potential. Single EV imaging that can measure the abundance of protein biomarkers in EVs can help in detecting the presence, stage, and progression of disease. Antibodies are typically used to detect EV proteins. Controlling the quality of antibody-based immunoassays can, however, be challenging, as they may exhibit unintended cross-reactivity with non-target proteins or variability in binding affinity across different batches, even for monoclonal antibodies. Here, we report short peptides that are a promising alternative to antibodies for detecting protein biomarkers in EVs. We describe an effort that combines a Peptide Binding Design (PepBD) algorithm and molecular-level simulations to identify peptides that can recognize (1) the extracellular domain of EpCAM (a known cancer biomarker) and (2) the extracellular domain of tetraspanin CD81(a protein commonly expressed on the surface of EVs). The peptides designed for EpCAM and CD81 were labeled with a fluorescent dye and their binding to the target protein was evaluated using fluorescence ELISA. The results demonstrated that one of the computationally designed peptides EP-2.1 exhibited an affinity for the target EpCAM protein comparable to that of an antibody. Further testing involved single EV imaging to gauge the peptides affinity towards EVs. Designed peptides for both the target proteins showed similar affinity as antibodies to EVs.

Therapeutic antibody efficacy is largely determined by the target epitope. In addition, off-target binding can result in unanticipated side-effects. Therefore, characterization of the epitope and binding specificity are critical in antibody discovery. Epitope binning provides low-resolution of an antibody epitope and is typically performed as a cross-blocking assay to group antibodies into overlapping or non-overlapping bins. Epitope mapping identifies the epitope with high resolution but requires low throughput methods. In addition to binning and mapping, there is a need for a scalable and predictive approach to reveal off-target binding early in antibody discovery to reduce the risk of in vivo side effects. Peptide microarrays are an information-rich platform for antibody characterization. However, the potential of peptide microarrays in early-stage antibody discovery has not been realized because they are not produced at the scale, quality and format needed for reliable high-throughput antibody characterization. A unified, peptide library platform for high-resolution antibody epitope binning, mapping and predictive off-target binding characterization is described here. This platform uses highly scalable array synthesis and photolithography to synthesize more than 3 million addressable peptides. These arrays conform to a microplate format and each synthesis is qualified with mass spectrometry. Using this platform, a scalable approach to early-stage epitope and specificity characterization, with prediction of off-target interaction(s), is demonstrated using a panel of anti-HER2 monoclonal antibodies. This study highlights the prospect of this platform to improve antibody discovery productivity by generating epitope and specificity information much earlier with potentially hundreds of antibody clones.

BackgroundAs the most abundant immunoglobulin in blood and the most common human isotype used for therapeutic monoclonal antibodies, the engagement and subsequent activation of its Fc receptors by IgGs are crucial for antibody function. While generally assumed to be relatively constant within subtypes, recent studies have shown the antibody variable regions to exert distal effects of modulating antibody-receptor interactions on many antibody isotypes. Such effects are also expected for IgG and its subtypes with the in-depth understanding of these V-region effects highly relevant for engineering antibodies, antibody purifications, and understanding to how robust the microbial immune evasion proteins are. MethodsIn this study, we created a panel of IgG2/IgG3/IgG4 antibodies by changing the VH family (VH1-7) frameworks while retaining the complementarity determining regions of Pertuzumab and measured the interaction of the IgGs with Fc{gamma}RIa, Fc{gamma}RIIaH167, Fc{gamma}RIIaR167, Fc{gamma}RIIb/c, Fc{gamma}RIIIaF176, Fc{gamma}RIIIaV176, Fc{gamma}RIIIbNA1, and Fc{gamma}RIIIbNA2 receptors alongside antibody superantigens proteins L and G using biolayer interferometry. ResultsThe library of 21 IgGs demonstrated that the VH frameworks influenced receptor binding sites on the constant region of the subtypes significantly, providing non-canonical interactions and non-interactions. However, there was minimal influence on the binding of bacterial B-cell superantigens Proteins L and G on the IgGs, showing their robustness against V-region effects. ConclusionsThese results demonstrate the importance of the V-regions during humanization of therapeutic antibodies that can confer or diminish FcR-dependent immune responses, while remaining both suitable and susceptible to the binding by bacterial antibody superantigens in antibody purification and be present with normal flora. STATEMENT OF SIGNIFICANCEIgGs are the predominant isotype for clinical and research applications. Despite the vast amount of research to study it, particularly on IgG1, there remains a gap in understanding how the variable regions and the receptor binding sites can influence one another in the other IgG subtypes, across the IgG subtypes with different hinges and makeup. This study investigates the effect of these variable regions on the engagement of receptors and also how bacterial antibody superantigens present in microflora and used in antibody purification can exert distal effects.

Dose selection and confirmation are critical tasks in the development of therapeutic antibodies. These tasks could become particularly challenging in the absence of robust pharmacodynamics biomarkers or at very flat dose-response curves. Although much knowledge has been acquired in the past decade, it remains uncertain which factors are relevant and how to select doses more rationally. In this study, we developed a quantitative metric, Therapeutic Exposure Affinity Ratio (TEAR), to retrospectively evaluate up to 60 approved antibodies and their therapeutic doses (TDs), and systematically assessed the factors that are relevant to antibody TDs and dose selection patterns. This metric supported us to analyze many factors that are beyond antibody pharmacokinetics and target binding affinity. Our results challenged the traditional perceptions about the importance of target turnovers and target anatomical locations in the selection of TDs, highlighted the relevance of an overlooked factor, antibody mechanisms of action. Overall, this study provided insights into antibody dose selection and confirmation in the development of therapeutic antibodies.