Retained DisplayTM

Discovering pMHC antibodies quickly and effectively.

Our Technology

The Retained DisplayTM (ReD) platform was developed in-house by Affinity’s founders Ben Kiefel and Matt Beasley. Using a completely different, patent-protected process to other antibody discovery platforms, the speed and flexibility of the platform enables it to find very rare binders against challenging targets.

ReD has been deployed to rapidly screen and isolate neutralizing antibodies specific for SARS-CoV-2.

Technology

Being large proteins, antibodies cannot enter cells due to their size. As a result, the current market for antibodies – valued around US$120 billion – is based entirely on targeting cell-surfaces and soluble proteins.

Most of the changes that occur in the transformation of a normal cell into a cancer cell take place behind the cell membrane making them impossible for ‘traditional’ antibodies to be useful.

Every protein inside every nucleated cell will be broken up into short peptides by the proteasome as part of natural protein turnover. These peptides are taken up into the endoplasmic reticulum where some of them are loaded into a carrier molecule called major histocompatibility complex (MHC) also referred to as human leucocyte antigen (HLA) in humans. The peptide-MHC complex is then transported to the cell surface providing a glimpse of what is happening within the cell.

The natural binding partner for a peptide-MHC complex is the T-cell receptor which has to be able to discriminate between peptide-MHC complexes on the basis of specific interactions with the peptide. Thus, cells that are infected by a virus or contain an altered protein can be detected and destroyed by T-cells.

Antibodies, like T-cell receptors, are from a family of proteins called immunoglobulins and both have similar structures consisting of two protein chains that together form the antigen, or target, binding site.

The challenge of targeting peptide-MHC complexes

Finding good antibodies against peptide-MHC complexes is extremely challenging because they are extremely rare – sometimes one in a hundred billion. This is because the antibody has to interact with several amino acids along the length of a short linear peptide to achieve selectivity. Large libraries of different antibodies are required, and it is essential that these rare binders are not lost during the screening process due to loss of diversity.

The Affinity difference

Affinity has designed and built a novel platform around its Retained Display (ReD) technology that is unique in its ability to consistently find quality binders against peptide-MHC complexes. It works because ReD is a ‘lossless’ system i.e. there is no loss of diversity through the discovery process and this is critical when trying to find very rare binders.

ReD is a unique antibody discovery engine that is quite distinct from either the use of transgenic animals or filamentous phage display.

ReD employs a lambdoid phage which has a number of advantages over filamentous phage display. The key points of difference between filamentous phage display and ReD are as follows:

  • Higher avidity panning of libraries to ensure capture of all clones that bind the target
  • High-speed cell sorting of the many captured clones using clonal cell-display of each binder
  • No loss of diversity during the panning and enrichment steps making ReD the first ‘lossless’ discovery platform – essential when looking for very rare binders
  • Due to its cell-display step, which employs high speed cell sorting, ReD is also incredibly fast achieving industry-leading speed for antibody discovery

Affinity’s libraries consist of single chain variable fragments (scFv) built on germ-line human antibody sequences and, therefore, require no humanization. The scFv are very stable and can readily be converted to IgG or other formats.

Affinity is happy to discuss the attributes of the ReD system in more detail with interested parties.

Affinity has demonstrated the utility of its scFv binders in bispecific format (anti-CD3) and in chimeric antigen receptor T-cells (CAR-T). This work has been conducted in-house and with our collaborators of global top institutions across a range of different cancers and targets, including neoantigens, human endogenous retroviruses (HERVs), cancer-testis antigens, and wild-type self-proteins.

T-cells and T-cell receptor-based approaches are increasingly attracting attention due to their ability to target intracellular proteins, although the clinical and manufacturing experience with these modalities is still limited compared to monoclonal antibodies. In addition, there are many targets for which it is difficult to find good T-cell receptors or T-cells. These include the majority of neoantigens (mutated proteins that occur in cancer) and self-proteins, for example PSA or p53. This is because any high avidity T-cell that can target a peptide from a self-protein is deleted in the thymus to prevent auto-immunity which occurs when the immune system attacks normal healthy tissue.

Antibodies are highly selective and generally have higher affinities than T-cell receptors. T-cell receptors can be engineered to increase their affinity although this is a lengthy and uncertain process.

Smaller antibody fragments such as scFv provide the option of manufacturing in microbial systems, such as in E. coli. This enables faster scale-up and a lower cost of manufacturing; a factor that can be important in response to emergent diseases, for example.

Targeting pMHC

Technology

Being large proteins, antibodies cannot enter cells due to their size. As a result, the current market for antibodies – valued around US$120 billion – is based entirely on targeting cell-surfaces and soluble proteins.

Most of the changes that occur in the transformation of a normal cell into a cancer cell take place within the cell membrane making them impossible for ‘traditional’ antibodies to be useful.

Every protein inside every nucleated cell will be broken up into short peptides by the proteasome as part of natural protein turnover. These peptides are taken up into the endoplasmic reticulum where certain of them are loaded into a carrier molecule called major histocompatibility complex (MHC) also referred to as human leucocyte antigen (HLA) in man. The peptide-MHC complex is then transported to the cell surface providing a glimpse of what is happening within the cell.

The natural binding partner for a peptide-MHC complex is the T-cell receptor which has to be able to discriminate between peptide-MHC complexes on the basis of specific interactions with the peptide. Thus, cells that are infected by a virus or contain an altered protein can be detected and destroyed by T-cells

Antibodies, like T-cell receptors, are from a family of proteins call immunoglobulins and both have similar structures consisting of two protein chains that together form the antigen, or target, binding site.

The challenge of targeting peptide-MHC complexes

Finding good antibodies against peptide-MHC complexes is extremely challenging because they are extremely rare – sometimes one in a hundred billion. This is because the antibody has to interact with several amino acids along the length of a short linear peptide to achieve selectivity. Large libraries of different antibodies are required, and it is essential that these rare binders are not lost during the screening process due to loss of diversity.

The Affinity difference

Affinity has designed and built a novel platform around its Retained Display (ReD) technology that is unique in its ability to consistently find quality binders against peptide-MHC complexes. It works because ReD is a ‘lossless’ system i.e. there is no loss of diversity through the discovery process and this is critical when trying to find very rare binders.

Introducing ReD

ReD is a unique antibody discovery engine that is quite distinct from either the use of transgenic animals or filamentous phage display.

ReD employs a lambdoid phage which has a number of advantages over filamentous phage display. The key points of difference between filamentous phage display and ReD are as follows:

  • Higher avidity panning of libraries to ensure capture of all clones that bind the target
  • High-speed cell sorting of the many captured clones using clonal cell-display of each binder
  • No loss of diversity during the panning and enrichment steps making ReD the first ‘lossless’ discovery platform – essential when looking for very rare binders
  • Due to its cell-display step, which employs high speed cell sorting, ReD is also incredibly fast achieveing industry leading speed for antibody discovery

Affinity’s libraries consist of single chain variable fragments (scFv) built on germ-line human antibody sequences and, therefore, require no humanization. The scFv are very stable and can readily be converted to IgG or other formats.

Affinity is happy to discuss the attributes of the ReD system in more detail with interested parties.

CAR-T and Bispecifics

Affinity has demonstrated the utility of its scFv binders in bispecific format (anti-CD3) and in chimeric antigen receptor T-cells (CAR-T). This work has been conducted in-house and with our collaborators of global top institutions across a range of different cancers and targets, including neoantigens, human endogenous retroviruses (HERVs), cancer-testis antigens, and wild-type self-proteins.

Benefits of scFvs/antibodies

T-cells and T-cell receptor-based approaches are increasingly attracting attention due to their ability to target intracellular proteins, although the clinical and manufacturing experience with these modalities is still limited compared to monoclonal antibodies. In addition, there are many targets for which it is difficult to find good T-cell receptors or T-cells. These include the majority of neoantigens (mutated proteins that occur in cancer) and self-proteins, for example PSA or p53. This is because any high avidity T-cell that can target a peptide from a self-protein is deleted in the thymus to prevent auto-immunity which occurs when the immune system attacks normal healthy tissue.

Antibodies are highly selective and generally have higher affinities than T-cell receptors. T-cell receptors can be engineered to increase their affinity although this is a lengthy and uncertain process.

Smaller antibody fragments such as scFv provide the option of manufacturing in microbial systems, such as in E. coli. This enables faster scale-up and a lower cost of manufacturing; a factor that can be important in response to emergent diseases, for example.

Cancer

Affinity has successfully screened against over 100 peptide-MHC complexes using ReD. We are partnering with top institutions globally to evaluate our binders and test their ability to kill cancers carrying the relevant mutations.

See our pipeline

COVID-19

We have deployed ReD to meet the COVID-19 challenge. In doing so we have identified a number of high-affinity binders which are capable of blocking the binding of the SARS-CoV-2 spike protein to the human ACE2 receptor. These antibodies are currently in live virus testing at the The Peter Doherty Institute for Infection and Immunity in Melbourne.

Learn more

Partnering with us

Affinity is seeking partnerships to fully exploit the potential of its technology whilst also building an in-house portfolio of products.

Contact us