Explosive growth of global therapeutic mAb market is expected to generate revenue > $300 billion by 2025. Prudent choice of predictive profiling assays during discovery is pivotal for minimizing attrition in late clinical development. Here, I am sharing my perspectives on an integrated screening paradigm for the selection and characterization of a truly first-in-class high affinity antibody against a novel prostate cancer target that is a single pass transmembrane protein.

GPCRs rely on membrane for proper folding, making their biochemical properties difficult to study. By displaying GPCRs in viral envelopes, we fabricated a Virion Display (VirD) array containing 315 non-olfactory human GPCRs for functional characterization. Using this array, we found that 10 of 20 anti-GPCR mAbs were ultra-specific. We believe that the VirD-GPCR array holds great potential for high-throughput screening for small molecule drugs, affinity reagents, and ligand deorphanization.

Recent technology advances are enabling highly efficient antibody discovery campaigns resulting in the identification of diverse antigen-specific antibody panels. Introduction of functional screening assays, early in the process, may become essential for prioritization of antibodies with therapeutic potential. In this talk, high throughput functional screening assays are presented as a part of integrated screening funnel, highlighting challenges and benefits of the early implementation of functional assays.

Fibroblast growth factor receptor 1 (FGFR1) is a promising therapeutic target for multiple pathologies including metabolic diseases and cancer. Targeting of FGFR1 may require an agonist or antagonist depending on the indication. We investigated the mechanism of action of anti-FGFR1 antibodies reported to be agonist or antagonist and described a novel functionally distinct FGFR1 active conformation, demonstrating that modulating the geometry of FGFR1 dimers can effectively change the signaling outputs and in vivo activity.

The limited number of suitable antigens has restricted the utility of antibody-based cancer therapy. Complementing bottom-up antigen discovery by transcriptomics and proteomics, we are pursuing top-down antigen discovery strategies based on the selection of antibody libraries against live cancer cells by phage display. Notoriously challenging due to the stickiness of phage, a new method, termed Fab biotinylation and capture (FBC), was developed. Following proof-of-concept, FBC was used for differential selection on target cells versus non-target cells followed by next-generation sequencing (NGS) and bioinformatic processing. Combining FBC and NGS was applied to antigen discovery in multiple myeloma and acute myeloid leukemia.

Emerging data suggest that approximately 25% of therapeutic MAbs in development are polyspecific and this can result in severe adverse events. We developed the Membrane Proteome Array (MPA) to de-risk MAb safety through specificity testing across an array of 6,000 native-conformation human membrane proteins. We will discuss the importance of early stage specificity testing and present case studies for antibody and cell therapies against SARS-CoV-2 Spike and other complex therapeutic targets.  

The small size of nanobodies enables genetic manipulation to incorporate protein tags. VUN400, a nanobody which recognizes the second extracellular loop of the chemokine CXCR4 receptor, was conjugated to the 11-amino acid HiBiT tag (VUN400-HiBiT) which complements LgBiT protein, forming full-length functional NanoLuc luciferase. Complemented luminescence was used to detect VUN400-HiBiT binding to CXCR4 expressed in HEK293 cells. VUN400-HiBiT binding to CXCR4 was prevented by orthosteric and allosteric ligands, allowing VUN400-HiBiT to be used as a probe to detect allosteric interactions with CXCR4. This demonstrated the high specificity offered by extracellular targeted nanobodies can be utilized to probe receptor pharmacology.

Adenoassociated viral vectors (AAV) are used in gene therapy, oncology, and for producing therapeutic antibodies in vivo. However, the broad tissue tropism of AAV still hampers their clinical development. We demonstrate that a membrane protein-specific nanobody can readily be inserted into a surface loop of the AAV capsid. This results in a 50-500 fold increased transduction of cells expressing the target membrane protein. We have verified the efficacy of this platform for a variety of cells expressing different target proteins, using different AAV serotypes displaying nanobodies directed against GPI-anchored, singlespan, or multispan transmembrane proteins.

VHH antibodies and their unique properties offer an alternative approach to targeting complex membrane targets. This platform has been successfully applied to identify a potent half-life extended VHH antibody antagonist to CX3CR1, a target that has been identified as highly attractive for several therapeutic interventions. Additionally, we discuss the application of this platform to other membrane targets, the benefits and limitations of this approach, and possible future directions.

Impaired protein stability or membrane trafficking underlies diverse ion channelopathies and represents an unexploited unifying principle to develop common treatments for otherwise dissimilar diseases. Ubiquitination limits ion channel surface density, but targeting this pathway for basic study or therapy is challenging because of its prevalent role in proteostasis. We developed engineered deubiquitinases that enable ubiquitin chain removal selectively from target proteins to rescue functional expression of disparate mutant ion channels underlying Long QT syndrome and cystic fibrosis. This talk will focus on targeted deubiquitination as a powerful protein stabilization method to correct diverse diseases caused by impaired ion channel trafficking.

Antibodies conjugated to bioactive compounds allow targeted delivery of therapeutics. We present a new type of conjugate that consists of a nanobody and a peptidic ligand for a G protein-coupled receptor (GPCR) which show biological activity superior to that of the parent fragment peptide in vitro and in mice. This approach can yield new ligands for cell surface receptors with properties superior to those previously provided by chemistry or nature.

Evolution of SARS-CoV-2 spike was slow at the beginning of pandemic. However, now major escape variants emerge which makes antigen generation highly challenging but rewarding if we develop therapeutics targeting the SARS-CoV-2 variants and other emerging coronaviruses. Achieving these goals requires strategic design of high-quality antigens that can be used as immunogens or screening reagents. This presentation will describe the challenges and present our design strategies for our pan-coronavirus program.

At TetraGenetics, Inc., we have developed a strategy for identifying functionally modulating antibodies targeting human ion channels. High-yield production of human channels using Tetrahymena thermophila-based TetraExpress platform is combined with a multi-platform antibody discovery approach, followed by screening and characterization in mammalian cells. We describe the discovery of monoclonal antibodies that modulate the activity of voltage-gated channels Kv1.3 and Nav1.8. 

Despite the high specificity of antibodies for protein targets, being able to target antigens specifically altered in the tumor environment has been challenging. Proteolysis is a driver of cancer and inflammation and we have developed new proteomics means to identify novel proteolytic events on cell surface proteins (Weeks et al., PNAS 2021). We have further shown it possible to target proteolytic neo-epitopes on cancer associated membrane proteins. In addition to binding membrane proteins with antibodies, we have recently shown it possible to degrade them by recruiting transmembrane E3 ligases to proteins of interest using bi-specific antibodies, a biologics technology akin to small molecule PROTACs, we call AbTACs (Cotton et al. JACS 2021).

Receptors relevant to CNS disorders typically have associated proteins discretely expressed in specific neuronal pathways; these accessory proteins provide a new dimension for drug discovery. Recent studies show that targeting a TARP auxiliary subunit of AMPA receptors selectively modulates neuronal excitability in specific forebrain pathways relevant to epilepsy. Other medicinally important ion channels, gated by glutamate, GABA, and acetylcholine, also have associated proteins, which may be druggable. This emerging pharmacology of receptor-associated proteins provides a new approach for improving drug efficacy while mitigating side effects.