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Protein (poly)peptides libraries

a technology of polypeptides and libraries, applied in the field of synthetic dna sequences, can solve the problems of not providing the possibility of improving the desired properties of the members in an easy and rapid manner, no general procedure available to improve the desired properties of the members, and winter invention does not provide for artificial variable regions

Inactive Publication Date: 2006-01-05
MORFOZIS AG
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Benefits of technology

[0022] In one embodiment, the removal of unfavorable interactions as described above, leads to enhanced expression of the modified (poly)peptides.
[0072] The corresponding amino acid sequences of two or more genes are aligned to each other in a way which maximizes the correspondence between identical or similar amino acid residues at all positions. These aligned sequences are termed homologous if the percentage of the Sum of identical and / or similar residues exceeds a defined threshold. This threshold is commonly regarded by those skilled in the art as being exceeded when at least 15 percent of the amino acids in the aligned genes are identical, and at least 30 percent are similar.

Problems solved by technology

All current recombinant methods which use libraries of proteins / (poly)peptides, e.g. antibodies, to screen for members with desired properties, e.g. binding a given ligand, do not provide the possibility to improve the desired properties of the members in an easy and rapid manner.
There is no general procedure available to improve these molecules further on.
Furthermore, the Winter invention does not provide for artificial variable region genes, which represent a whole family of structurally similar natural genes, and which can be assembled from synthetic DNA oligonucleotides.
Furthermore, this approach has the disadvantage that the genes of all antibodies obtained in the screening procedure have to be completely sequenced, since, except for the PCR priming regions, no additional sequence information about the library members is available.
This is time and labor intensive and potentially leads to sequencing errors.
It has been suggested that a single universal framework may be useful to build antibody libraries, but no approach has yet been successful.
Another problem lies in the production of reagents derived from antibodies.
Functional protein may be obtained from the latter in modest yields by a laborious and time-consuming refolding process.
The factors influencing antibody expression levels are still only poorly understood.
Folding efficiency and stability of the antibody fragments, protease lability and toxicity of the expressed proteins to the host cells often severely limit actual production levels, and several attempts have been tried to increase expression yields.
Nevertheless, these strategies are only applicable to a few antibodies.
Furthermore, this approach enables (i), adapting the codon usage of the genes to that of highly expressed genes in any desired host cell and (ii), analyzing all possible pairs of antibody light (L) and heavy (H) chains in terms of interaction preference, antigen preference or recombinant expression titer, which is virtually impossible using the complete collection of antibody genes of an organism and all combinations thereof.

Method used

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Examples

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example 1

Design of a Synthetic Human Combinatorial Antibody Library (HuCAL)

[0123] The following example describes the design of a fully synthetic human combinatorial antibody library (HuCAL), based on consensus sequences of the human immunoglobulin repertoire, and the synthesis of the consensus genes. The general procedure is outlined in FIG. 1.

1.1 Sequence Database

1.1.1 Collection and Alignment of Human Immunoglobulin Sequences

[0124] In a first step, sequences of variable domains of human immunoglobulins have been collected and divided into three sub bases: V heavy chain (VH), V kappa (Vκ) and V lambda (Vλ). For each sequence, the gene sequence was then translated into the corresponding amino acid sequence. Subsequently, all amino acid sequences were aligned according to Kabat et al. (1991). In the case of Vλ sequences, the numbering system of Chuchana et al. (1990) was used. Each of the three main databases was then divided into two further sub bases: the first sub base contained all...

example 2

Cloning and Testing of a HuCAL-Based Antibody Library

[0154] A combination of two of the synthetic consensus genes was chosen after construction to test whether binding antibody fragments can be isolated from a library based on these two consensus frameworks. The two genes were clones as a single-chain Fv (scFv) fragment, and a VH-CDR3 library was inserted. In order to test the library for the presence of functional antibody molecules, a selection procedure was carried out using the small hapten fluorescein bound to BSA (FITC-BSA) as antigen.

2.1 Cloning of the HuCAL VH3-Vk2 scFv Fragment

[0155] In order to test the design of the consensus genes, one randomly chosen combination of synthetic light and heavy gene (HuCAL-Vκ2 and HuCAL-VH3) was used for the construction of a single-chain antibody (scFv) fragment. Briefly, the gene segments encoding the VH3 consensus gene and the CH1 gene segment including the CDR3-framework 4 region, as well as the Vκ2 consensus gene and the Cκ gene se...

example 3

HuCAL H3κ2 Library Against a Collection of Antigens

[0166] In order to test the library used in Example 2 further, a new selection procedure was carried out using a variety of antigens comprising β-estradiol, testosterone, Lewis-Y epitope (LeY), interleukin-2 (IL-2), lymphotoxin-β (LT-β), E-selectin ligand-1 (ESL-1), and BSA.

3.1 Biopanning

[0167] The library and all procedures were identical to those described in Example 2. The ELISA plates were coated with β-estradiol-BSA (100 μg / ml), testosterone-BSA (100 μg / ml), LeY-BSA (20 μg / ml) IL-2 (20 μg / ml), ESL-1 (20 μg / ml) and BSA (100 μg / ml), LT-β (denatured protein, 20 μg / ml). In the first two rounds, bound phages were eluted with 0.1 M triethylamine (TEA) at RT for 10 minutes. In the case of BSA, elution after three rounds of panning was carried out with addition of BSA in a concentration of 100 μg / ml in PBS. In the case of the other antigens, third round elution was done with 0.1 M triethylamine. In all cases except LeY, enrichment ...

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Abstract

The present invention relates to synthetic DNA sequences which encode one or more collections of homologous proteins / (poly)peptides, and methods for generating and applying libraries of these DNA sequences. In particular, the invention relates to the preparation of a library of human-derived antibody genes by the use of synthetic consensus sequences which cover the structural repertoire of antibodies encoded in the human genome. Furthermore, the invention relates to the use of a single consensus antibody gene as a universal framework for highly diverse antibody libraries.

Description

FIELD OF THE INVENTION [0001] The present invention relates to synthetic DNA sequences which encode one or more collections of homologous proteins / (poly)peptides, and methods for generating and applying libraries of these DNA sequences. In particular, the invention relates to the preparation of a library of human-derived antibody genes by the use of synthetic consensus sequences which cover the structural repertoire of antibodies encoded in the human genome. Furthermore, the invention relates to the use of a single consensus antibody gene as a universal framework for highly diverse antibody libraries. BACKGROUND TO THE INVENTION [0002] All current recombinant methods which use libraries of proteins / (poly)peptides, e.g. antibodies, to screen for members with desired properties, e.g. binding a given ligand, do not provide the possibility to improve the desired properties of the members in an easy and rapid manner. Usually a library is created either by inserting a random oligonucleoti...

Claims

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Application Information

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IPC IPC(8): C12Q1/68C12P19/34C12N15/09C07K1/04C07K14/47C07K16/00C12N1/15C12N1/19C12N1/21C12N5/10C12N15/10C12N15/13C12N15/62C12N15/70C12P21/02C40B40/02G01N33/53
CPCC07K1/047C40B40/02C07K16/005C07K16/18C07K16/242C07K16/26C07K16/2854C07K16/2896C07K16/44C07K2317/21C07K2317/565C07K2317/622C07K2319/00C12N15/10C12N15/1037C07K16/00
Inventor ACHIM, KNAPPIKPACK, PETERLIMING, GESIMON, MORONEYANDREAS, PLUCKTHUN
Owner MORFOZIS AG
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