a ‘one-on-many’ ‘analyte-on-ligand’ assay format that not only speeds up kinetic measurements, but is also very efficient on antigen consumption, necessitating only a single aliquot per analyte con- centration to perform a kinetic analysis on a large array of antibodies. Indeed, measurements per- formed on Carterra’s Array SPR biosensor support 384 antibody arrays as standard and deliver high quality binding data, as shown in Figure 1.

Using SPR to characterise the binding specificity of antibody interactions The region of an antigen that is recognised by an antibody is referred to as the ‘epitope’. Knowing an antibody’s epitope is highly relevant to the suc- cess of a therapeutic antibody programme because it largely dictates an antibody’s biological function or mechanism of action (MOA). An antibody’s epi- tope is an innate property that can neither be pre- dicted nor rationally designed by in silico methods, and so selecting an antibody with an appropriate epitope to fulfil a given therapeutic goal is an empirical process. Furthermore, since an anti- body’s epitope cannot be shifted or optimised by engineering in a rational way, it is advantageous to survey the epitope landscape of an antibody library at the earliest possibility to identify and move for- ward only those clones exhibiting the most appro- priate epitopes or a variety of epitopes that can be tested in functional assays to converge upon leads. From an intellectual property perspective, claiming novel epitopes enables companies to have an edge in the fiercely competitive market of therapeutic antibody discovery, with multiple companies often working on the same targets, as evidenced by the clinical pipeline. For example, the immune check- point modulators PD-1 (programmed death recep- tor-1) and its ligand (PD-L1) remain popular tar- gets for treating cancer, despite five antibodies tar- geting the PD-1 pathway already on the market. Currently, in clinical development there are 21 molecules targeting PD-1, including five in late- stage clinical studies and nine antibodies targeting PD-L113. Another example is in the prevention of migraine, where multiple companies have antibod- ies targeting CGRP (calcitonin gene-related pep- tide) or its receptor in late-stage clinical trials14. There are many analytical techniques available

for characterising an antibody’s epitope, with the gold standard for precise epitope determination provided by atomic-level structural data produced by x-ray crystallography and cryo-electron microscopy. However, these methods are labour- intensive and slow, and therefore used as confirma- tory tools, rather than research-based ones. More

Drug Discovery World Summer 2018

practical methods include epitope mapping using libraries of antigenic variants produced by display methods15,16. A facile and quick way of identifying antibodies

that cluster into epitope families is provided by epi- tope binning experiments which can be performed in high throughput and with low sample consump- tion on biosensors. Epitope binning is a competi- tive assay where antibodies are tested in a pairwise and combinatorial manner for their ability to bind simultaneously to their specific antigen. If both antibodies can bind at the same time, they are pre- sumed to target distinct, non-overlapping epitopes, whereas if one appears to block the other, it is inferred that they compete for overlapping or sim- ilar epitopes. With the now routine implementa- tion of label-free biosensors for epitope binning, there is a need for higher throughput platforms that enable more antibodies to be tested in a single assay to explore the depth and breadth of an anti- body campaign in a comprehensive manner. BLI- based platforms are commonly used for epitope binning but since sample consumption scales with the size of the antibody panel investigated, these assays are often limited to rather small panels17 (Figure 2). In contrast, Array SPR methods enable larger panels to be analysed on a single chip with published examples demonstrating these analyses on 96-18, 192-12 (Figure 3), and 384-antibody arrays19. The demand for higher throughput analytics is

needed to support the paradigm shift that is emerging in the industry towards a deeper appre- ciation of the epitope diversity offered within an antibody library by applying higher resolution and higher throughput methods for epitope character- isation at the earliest stages of research. This enables the identification of uniquely-suited clones and minimises the need for their extensive engi- neering, which streamlines library-to-leads and ultimately cuts costs to patients by delivering medicines faster.


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17 Sapparapu, G et al. Neutralizing human antibodies prevent Zika virus replication and fetal disease in mice. Nature 2016 Nov; 540(7633): 443-447. 18Abdiche, YN, Miles, A, Eckman, J, Foletti, D, Van Blarcom, TJ, Yeung, YA, Pons, J, Rajpal, A. High-throughput epitope binning assays on label-free array-based biosensors can yield exquisite epitope discrimination that facilitates the selection of monoclonal antibodies with functional activity. PLoS One. 2014 Mar 20;9(3):e92451. 19 Sivasubramanian, Arvind, Estep, Patricia, Lynaugh, Heather, Yu, Yao, Miles, Adam, Eckman, Josh, Schutz, Kevin, Piffath, Crystal, Boland, Nadthakarn, Hurley Niles, Rebecca, Durand, Stéphanie, Boland, Todd, Vásquez, Maximiliano, Xu, Yingda and Abdiche, Yasmina (2016). Broad epitope coverage of a human in vitro antibody library. mAbs, 9:1, 29-42.

Dr Yasmina Noubia Abdiche is Chief Scientific Officer at Carterra. Dr Abdiche joined Carterra as CSO in 2016 after 12.5 years’ experience in the pharmaceutical industry at Rinat-Pfizer, where she led a group of analytical scientists that applied label-free biosensors to the discovery of therapeu- tic antibodies. Dr Abdiche is co-inventor of several therapeutic antibodies in clinical trials.


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