# US 7,608,410 B2 · Method of improving T cell receptors

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- Number: US 7,608,410 B2
- Document ID: US7608410B2
- Status: Granted
- Kind: B2
- Application number: 12/246,607
- Filed: 2008-10-07
- Published: 2009-02-26
- Granted: 2009-10-27
- Earliest claimed: 2004-05-19
- Assignees: Immunocore Limited
- Applicants: Lucy Boulter, legal representative
- Inventors: Steven Mark Dunn; Yi Li; Jonathan Michael Boulter
- Web page: https://patentgrep.com/patent/US7608410B2

## CPC

- C40B 40/02: Libraries contained in or displayed by microorganisms, e.g. bacteria or animal cells; Libraries contained in or displayed by vectors, e.g. plasmids; Libraries containing only microorganisms or vectors
- C07K 14/7051: {T-cell receptor (TcR)-CD3 complex}
- C12N 15/1037: {Screening libraries presented on the surface of microorganisms, e.g. phage display, E. coli display}
- C40B: COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES (in silico combinatorial libraries of nucleic acids, proteins or peptides G16B35/00; in silico combinatorial chemistry G16C20/60)
- C07K: PEPTIDES (peptides in foodstuffs A23; obtaining protein compositions for foodstuffs, working-up proteins for foodstuffs A23J; preparations for medicinal purposes A61K; peptides containing beta-lactam rings C07D; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, C07D; ergot alkaloids of the cyclic peptide type C07D519/02; macromolecular compounds having statistically distributed amino acid units in their molecules, i.e. when the preparation does not provide for a specific; but for a random sequence of the amino acid units, homopolyamides and block copolyamides derived from amino acids C08G69/00; macromolecular products derived from proteins C08H1/00; preparation of glue or gelatine C09H; single cell proteins, enzymes C12N; genetic engineering processes for obtaining peptides C12N15/00; compositions for measuring or testing processes involving enzymes C12Q; investigation or analysis of biological material G01N33/00)
- C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00)

## Abstract

A method of increasing the affinity and/or decreasing the off-rate of a given TCR specific for a given target pMHC, comprising creating a plurality of TCRs having an α chain CDR2 sequence and/or a β chain CDR2 sequence different from the corresponding CDR2 sequence(s) of the given TCR but having the same α and β CDR1 and CDR3 sequences as the given TCR, determining the affinity and/or off-rate of members of said plurality of TCRs for the target pMHC, and selecting one or more members having at least a 10-fold greater affinity for the target pMHC than the given TCR and/or a 10-fold slower off-rate for the target pMHC than the given TCR.

## Claims

### Claim 1

A method of increasing the affinity and/or decreasing the off-rate of a given TCR specific for a given target pMHC, comprising creating a plurality of TCRs having an α chain CDR2 sequence and/or a β chain CDR2 sequence different from the corresponding CDR2 sequence(s) of the given TCR but having the same α and β CDR1 and CDR3 sequences as the given TCR, determining the affinity and/or off-rate of members of said plurality of TCRs for the target pMHC, and selecting one or more members having at least a 10-fold greater affinity for the target pMHC than the given TCR and/or a 10-fold slower off-rate for the target pMHC than the given TCR.

### Claim 2 (depends on 1)

The method of claim 1, comprising:
(a) creating a first plurality of TCRs which, relative to the given TCR, are mutated in the α chain CDR2 sequence but not the β chain CDR2 sequence,
(b) separately creating a second plurality of TCRs which, relative to the given TCR, are mutated in the β chain CDR2 sequence but not the α chain CDR2 sequence,
(c) determining the affinity and/or off-rate of members of said first and second pluralities of TCRs for the target pMHC, and selecting one or more members of each plurality having at least a 10-fold greater affinity for the target pMHC than the given TCR and/or a 10-fold slower off-rate for the target pMHC than the given TCR,
(d) determining the CDR2 sequences of the selected members of each plurality,
(e) creating one or more TCRs each having an α chain CDR2 sequence of the first plurality and a β chain CDR2 sequence of the second plurality, and
(f) determining the affinity and/or off-rate of the TCR or TCRs created in step (e) for the target pMHC, and selecting one or more thereof having at least a 10-fold greater affinity for the target pMHC than the given TCR and/or a 10-fold slower off-rate for the target pMHC than the given TCR.

### Claim 3 (depends on 1)

The method of claim 1, comprising:
(a) providing nucleic acid coding for both the β and β chains of the given TCR,
(b) subjecting said nucleic acid to mutagenesis of one or more codons of the α chain CDR2 sequence and one or more codons of the β chain CDR2 sequence,
(c) from the mutated nucleic acid of step (b) creating a plurality of TCRs which, relative to the given TCR, are mutated in one or more amino acids of the α chain CDR2 sequence and one or more amino acids of the β chain CDR2 sequence, and
(d) determining the affinity and/or off-rate of members of said plurality of TCRs for the target pMHC, and selecting one or more members having at least a 10-fold greater affinity for the target pMHC than the given TCR and/or a 10-fold slower off-rate for the target pMHC than the given TCR.

### Claim 4 (depends on 3)

The method of claim 3 wherein in step (b) the said nucleic acid is subjected to mutagenesis of up to three consecutive codons of the α chain CDR2 sequence and up to three consecutive codons of the β chain CDR2 sequence, and in step (c) a plurality of TCRs is created which, relative to the given TCR, are mutated in up to 3 consecutive amino acids of the α chain CDR2 sequence and up to three consecutive amino acids of the β chain CDR2 sequence.

### Claim 5 (depends on 1)

The method of claim 1 wherein the said affinities and/or off-rates are determined by Surface Plasmon Resonance.

### Claim 6 (depends on 1)

The method of claim 1 wherein one or more TCRs having at least a 100-fold greater affinity and/or 100-fold slower off-rate for the target pMHC than the given TCR is/are selected.

### Claim 7 (depends on 1)

The method of claim 1 wherein one or more TCRs having at least a 500-fold greater affinity and/or 500-fold slower off-rate for the target pMHC than the given TCR is/are selected.

### Claim 8 (depends on 1)

The method of claim 1 wherein the TCRs for affinity and/or on/off rate determination are created in soluble form.

### Claim 9 (depends on 1)

The method of claim 1 wherein the TCRs for affinity and on/off rate determination are created as a diverse library of phage-displayed αβ dimeric TCRs.

### Claim 10 (depends on 9)

The method of claim 9 wherein the phage-displayed αβ dimeric TCRs comprise
a first polypeptide wherein a sequence corresponding to a TCR α chain variable domain sequence is fused to the N terminus of a sequence corresponding to a TCR α chain constant domain extracellular sequence, and
a second polypeptide wherein a sequence corresponding to a TCR β chain variable domain sequence fused to the N terminus a sequence corresponding to a TCR β chain constant domain extracellular sequence,
the first and second polypeptides being linked by a disulfide bond which has no equivalent in native αβ T cell receptors, and one of said first or second polypeptides being linked by a peptide bond at its C-terminus to a surface exposed amino acid residue of the phage particle.

### Claim 11 (depends on 9)

The method of claim 9 wherein the phage-displayed αβ dimeric TCRs comprise
a first polypeptide wherein a sequence corresponding to a TCR α chain variable domain sequence is fused to the N terminus of a sequence corresponding to a TCR α chain constant domain extracellular sequence, and
a second polypeptide wherein a sequence corresponding to a TCR β chain variable domain sequence is fused to the N terminus a sequence corresponding to a TCR β chain constant domain extracellular sequence,
the first and second polypeptides being linked by a disulfide bond between cysteine residues substituted for Thr 48 of exon 1 of TRAC*01 and Ser 57 of exon 1 of TRBC1*01 or TRBC2*01 or the non-human equivalent thereof, one of said first or second polypeptides being linked by a peptide bond at its C-terminus to a surface exposed amino acid residue of the phage particle.

### Claim 12 (depends on 1)

The method of claim 1 wherein said plurality of TCRs is created as a diverse library of ribosome-displayed αβ single chain TCRs.

### Claim 13 (depends on 9)

The method of claim 9 wherein, for the purpose of determining the affinities and/or off-rates of library members which bind to the target pMHC and selecting those which have the desired affinities and/or off-rates
(i) several members of the library are contacted in parallel with the target pMHC and members which bind to the pMHC are identified,
(ii) members identified in step (i) are contacted in series with the target pMHC, and their affinities for the pMHC assessed,
(iii) one or more members having the desired affinity assessed in step (ii) are selected, and the CDR2 sequences of the displayed TCRs determined,
(iv) soluble form TCRs incorporating the thus-determined CDR2 sequences, are created,
(vi) the affinities and/or the off-rate for the target pMHC of these TCRs are redetermined and or determined as the case may be, and
(vii) one or more TCRs having the desired affinity and/or off-rate determined in step (vi) are selected.