Generation 3 Platform

Specifica’s Generation 3 Library Platform has quality built in by design. Developability, extremely high diversity, and the exclusion of sequence liabilities are intrinsic to the five sub-libraries making up the Platform, each of which is based on a therapeutic antibody scaffold chosen for its biophysical properties, lack of liabilities and germline gene variety.

Diversity is all derived from natural CDR sequences: HCDR3s are amplified directly from purified B cells, while replicated natural CDRs, derived from Specifica’s databases, are used for the rest.

Visionary antibody technologies

Why Generation 3?

Generation 3

  • B cells purified from Leukopaks
  • Amplification of B cell HCDR3s
  • 5 of 6 CDRs replicated natural
  • Developable clinical scaffolds
  • All but HCDR3 sequence liabilities purged
  • NGS quality control
  • HCDR3 diversity >108

Generation 2

  • B cells purified from Leukopaks
  • Amplification of VH / VL
  • Individual primer pairs
  • Biased towards better V genes
  • Sequence liabilities at natural frequencies
  • NGS quality control
  • HCDR3 Diversity: 107-8

Generation 1

  • Non purified peripheral B cells
  • Amplification of VH / VL
  • Pooled primers
  • Unbiased V genes
  • Sequence liabilities at natural frequencies
  • No NGS quality control
  • HCDR3 Diversity: 3×106

Library design

The use of natural CDR sequences alone, rather than combinatorial diversity, ensures correct folding, avoids co-variance violations, and allows the complete elimination of sequence based liabilities for five of the six CDRs.

As a result of the high functionality of our Generation 3 Library Platform, you can expect a broad diversity of different antibodies from your selections, most of which will have affinities below 10 nM, combined with developability properties usually at least as good as the clinical candidate antibodies from which they were derived.

We construct each Generation 3 library de novo, ensuring your library comprises a unique combination of naturally replicated CDRs, combined with at least one hundred million unique HCDR3s derived from a donor pool used only once, guaranteeing each supplied Generation 3 Library Platform is one of a kind.

Affinity

The majority of antibodies selected directly from the Generation 3 scFv Library using the combined phage and yeast protocol have affinities below 10nM, with ~20% having affinities in the sub-nanomolar range.

Developability

Inherent within the design and construction of the Generation 3 Platform is the ability to select high affinity, drug-like, therapeutic antibodies directly from the naive libraries, without the need for downstream optimization.

Confirmation of desired developability characteristics of selected antibodies was assessed by the expression of full length IgGs from selected antibodies and testing for: HEK titer, Tm, salt-gradient affinity capture self-interaction nanoparticle spectroscopy, ELISA on a panel of commonly used targets, cross-interaction chromatography and size-exclusion chromatography within the context of accelerated stability.

All full length IgG tested to date behave as well as, or better, than the therapeutic scaffolds from which they are derived.

Broad Diversity

Antibodies selected from our Generation 3 Library Platform show broad paratopic diversity by next generation sequencing of antibody populations fully positive for targets of interest.

We translate the extensive sequence dissimilarity into clontoypes, or clusters, using proprietary machine learning algorithms. Each clonotype is made up of one to fifty different but related sequences.

Our selection pipeline usually identifies five hundred to five thousand different clonotypes, with surprisingly large Levenshtein distances between different clonotypes, as illustrated in the figures.

This extensive clonotypic diversity provides antibodies against a wide variety of target epitopes important for drug efficacy, as well as variants within the clonotypes that allow exploration of the role of affinity modulation.

Paratopic diversity can be maximized still further if the sub-libraries making up the platform are used separately, rather than combined.

Levenshtein distances between different antibody clonotypes selected against a therapeutic target for differing numbers of CDRs, from all six (right) to HCDR3 only (left).

Continue Exploring

Go Back

Continue Exploring

Read More