Heteroclitic analogs and related methods

1. A method of producing a polypeptide of 9 to 20 amino acids in length comprising a heteroclitic analog of a Major Histocompatibility Complex (MHC) class I immunogenic epitope,

wherein said heteroclitic analog has enhanced immunogenicity compared to said epitope,

said method comprising:

(a) identifying a MT-IC class I immunogenic epitope from a protein antigen comprising a formula (A),

wherein formula (A) is Rn-R2-R3-R4-R5-R6-R7- . . . Rx,

Rn is the N-terminal amino acid,

Rx is the C-terminal amino acid,

x=8-11 such that Rx can be from the eighth to the eleventh amino acid residue from Rn,

R2 is a primary anchor residue of an A2 supermotif selected from the group consisting of L, I, V, M, A, T and Q,

Rx is a primary anchor residue of an A2 supermotif selected from the group consisting of L, I, V, M, A and T, and

(b) designing predicted analogs of said epitope having a formula (B) identical to said formula (A) except having one or more conservative or semi-conservative amino acid substitutions, in comparison to the original amino acid(s) at only R3 and/or R5 and/or R7,

(c) producing the predicted analogs of step (b) by introducing one or more conservative or semi-conservative amino acid substitutions, in comparison to the original amino acid(s) at only R3 and/or R5 and/or R7, wherein if said residue of said epitope is A, said conservative amino acid of said analog is S, T, P or G; if said residue of said epitope is C, said conservative amino acid of said analog is V, T, or A; if said residue of said epitope is D, said conservative amino acid of said analog is N, E, or Q; if said residue of said epitope is E, said conservative amino acid of said analog is Q, N, D, or H; if said residue of said epitope is F; said conservative amino acid of said analog is L, Y, I, M or V; if said residue of said epitope is G; said conservative amino acid of said analog is S, A, T, D or P; if said residue of said epitope is H; said conservative amino acid of said analog is Q, E, or N; if said residue of said epitope is I; said conservative amino acid of said analog is L, M, F, or V; if said residue of said epitope is K; said conservative amino acid of said analog is R, Q, or H; if said residue of said epitope is L; said conservative amino acid of said analog is I, M, F, or V; if said residue of said epitope is M; said conservative amino acid of said analog is L, I, V, or F; if said residue of said epitope is N; said conservative amino acid of said analog is D, E, Q, or H; if said residue of said epitope is P; said conservative amino acid of said analog is T, S, or A; if said residue of said epitope is Q; said conservative amino acid of said analog is E, H, N, or K; if said residue of said epitope is R; said conservative amino acid of said analog is K, H, or Q; if said residue of said epitope is S; said conservative amino acid of said analog is T, G, A, P or N; if said residue of said epitope is T; said conservative amino acid of said analog is P, S, A, or N; if said residue of said epitope is V; said conservative amino acid of said analog is L, I, or M; if said residue of said epitope is W; said conservative amino acid of said analog is F, Y, L, or M; and if said residue of said epitope is Y, said conservative amino acid of said analog is F or W; and wherein if said residue of said epitope is A, said semi-conservative amino acid of said analog is C, V, D, M, N, E, Q, H, or Y; if said residue of said epitope is C, said semi-conservative amino acid of said analog is S, P, I, Y, N, F, G, M, H, or D; if said residue of said epitope is D, said semi-conservative amino acid of said analog is T, S, H, G, P, A, K, R, or C; if said residue of said epitope is E, said semi-conservative amino acid of said analog is T, K, P, R, S, V, G, A, or M; if said residue of said epitope is F, said semi-conservative amino acid of said analog is W, H, C, T, R, or A; if said residue of said epitope is G, said semi-conservative amino acid of said analog is N, E, Q, H, C, or V; if said residue of said epitope is H, said semi-conservative amino acid of said analog is R, K, P, D, S, T, Y, M, or V; if said residue of said epitope is 1, said semi-conservative amino acid of said analog is Y, T, H, A, C, K, P, Q, or R; if said residue of said epitope is K, said semi-conservative amino acid of said analog is N, E, D, M, T, S, P, I, L, or Y; if said residue of said epitope is L, said semi-conservative amino acid of said analog is Y, H, Q, W, T, A, K, or P; if said residue of said epitope is M, said semi-conservative amino acid of said analog is K, Q, R, Y, H, A, T, P, W, or C; if said residue of said epitope is N, said semi-conservative amino acid of said analog is T, S, K, P, R, A, G, or V; if said residue of said epitope is P, said semi-conservative amino acid of said analog is H, Q, N, D, E, G, V, C, or M; if said residue of said epitope is Q, said semi-conservative amino acid of said analog is D, R, P, M, T, V, S, or A; if said residue of said epitope is R, said semi-conservative amino acid of said analog is E, N, M, D, P, W, S, T, I, L, or Y; if said residue of said epitope is S, said semi-conservative amino acid of said analog is D, C, E, H, Q, or K; if said residue of said epitope is T, said semi-conservative amino acid of said analog is D, E, G, H, Q, V, C, K, or M; if said residue of said epitope is V, said semi-conservative amino acid of said analog is P, T, F, A, C, H, Q, E, N, or S; if said residue of said epitope is W, said semi-conservative amino acid of said analog is R, I, H, V, K, Q, S, A, P, or T; and if said residue of said epitope is Y, said semi-conservative amino acid of said analog is H, M, L, T, I, C, V, P, A, N, Q, S, K or R;

(d) performing an analysis to identify analogs that render heteroclitic activity to said epitope as measured by an increased ability to elicit a T cell response, and

(e) producing a polypeptide of 9 to 20 amino acids in length comprising an analog with heteroclitic activity, wherein said method does not entail screening analogs containing random amino acid substitutions.

2. The method of claim 1 , wherein said analog exhibits at least 50% increased potency for a specific T-cell compared to said epitope.

3. The method of claim 1 , wherein only one substitution is introduced.

4. The method of claim 3 , wherein the substitution is a conservative substitution.

5. The method of claim 3 , wherein the substitution is a semi-conservative substitution.

6. The method of claim 1 , wherein the peptide comprising said analog induces both Th1 and Th2 cytokines when said analog is bound by an HLA Class I molecule and contacted with a cytotoxic T lymphocyte (CTL).

7. The method of claim 1 , wherein said epitope is derived from a viral antigen, a tumor-associated antigen, a parasitic antigen, a bacterial antigen or a fungal antigen.

8. A method of producing a polypeptide of 9 to 20 amino acids in length comprising a heteroclitic analog of a Major Histocompatibility Complex (MHC) class I immunogenic epitope,

wherein said heteroclitic analog has enhanced immunogenicity compared to said epitope,

said method consisting of:

(a) identifying a MHC class I immunogenic epitope from a protein antigen comprising a formula (A),

wherein formula (A) is Rn-R2-R3-R4-R5-R6-R7- . . . Rx,

Rn is the N-terminal amino acid,

Rx is the C-terminal amino acid,

x=8-11 such that Rx can be from the eighth to the eleventh amino acid residue from Rn,

R2 is a primary anchor residue of an A2 supermotif selected from the group consisting of L, I, V, M, A, T and Q,

Rx is a primary anchor residue of an A2 supermotif selected from the group consisting of L, I, V, M, A and T, and

(b) designing predicted analogs of said epitope having a formula (B) identical to said formula (A) except having one or more conservative or semi-conservative amino acid substitutions, in comparison to the original amino acid(s) at only R3 and/or R5 and/or R7,

(c) producing the predicted analogs of step (b) by introducing one or more conservative or semi-conservative amino acid substitutions, in comparison to the original amino acid(s) at only R3 and/or R5 and/or R7, wherein if said residue of said epitope is A, said conservative amino acid of said analog is S, T, P or G; if said residue of said epitope is C, said conservative amino acid of said analog is V, T, or A; if said residue of said epitope is D, said conservative amino acid of said analog is N, E, or Q; if said residue of said epitope is E, said conservative amino acid of said analog is Q, N, D, or H; if said residue of said epitope is F; said conservative amino acid of said analog is L, Y, I, M or V; if said residue of said epitope is G; said conservative amino acid of said analog is S, A, T, D or P; if said residue of said epitope is H; said conservative amino acid of said analog is Q, E, or N; if said residue of said epitope is I; said conservative amino acid of said analog is L, M, F, or V; if said residue of said epitope is K; said conservative amino acid of said analog is R, Q, or H; if said residue of said epitope is L; said conservative amino acid of said analog is I, M, F, or V; if said residue of said epitope is M; said conservative amino acid of said analog is L, I, V, or F; if said residue of said epitope is N; said conservative amino acid of said analog is D, E, Q, or H; if said residue of said epitope is P; said conservative amino acid of said analog is T, S, or A; if said residue of said epitope is Q; said conservative amino acid of said analog is E, H, N, or K; if said residue of said epitope is R; said conservative amino acid of said analog is K, H, or Q; if said residue of said epitope is S; said conservative amino acid of said analog is T, G, A, P or N; if said residue of said epitope is T; said conservative amino acid of said analog is P, S, A, or N; if said residue of said epitope is V; said conservative amino acid of said analog is L, I, or M; if said residue of said epitope is W; said conservative amino acid of said analog is F, Y, L, or M; and if said residue of said epitope is Y, said conservative amino acid of said analog is F or W; and wherein if said residue of said epitope is A, said semi-conservative amino acid of said analog is C, V, D, M, N, E, Q, H, or Y; if said residue of said epitope is C, said semi-conservative amino acid of said analog is S, P, I, Y, N, F, G, M, H, or D; if said residue of said epitope is D, said semi-conservative amino acid of said analog is T, S, H, G, P, A, K, R, or C; if said residue of said epitope is E, said semi-conservative amino acid of said analog is T, K, P, R, S, V, G, A, or M; if said residue of said epitope is F, said semi-conservative amino acid of said analog is W, H, C, T, R, or A; if said residue of said epitope is G, said semi-conservative amino acid of said analog is N, E, Q, H, C, or V; if said residue of said epitope is H, said semi-conservative amino acid of said analog is R, K, P, D, S, T, Y, M, or V; if said residue of said epitope is I, said semi-conservative amino acid of said analog is Y, T, H, A, C, K, P, Q, or R; if said residue of said epitope is K, said semi-conservative amino acid of said analog is N, E, D, M, T, S, P, I, L, or Y; if said residue of said epitope is L, said semi-conservative amino acid of said analog is Y, H, Q, W, T, A, K, or P; if said residue of said epitope is M, said semi-conservative amino acid of said analog is K, Q, R, Y, H, A, T, P, W, or C; if said residue of said epitope is N, said semi-conservative amino acid of said analog is T, S, K, P, R, A, G, or V; if said residue of said epitope is P, said semi-conservative amino acid of said analog is H, Q, N, D, E, G, V, C, or M; if said residue of said epitope is Q, said semi-conservative amino acid of said analog is D, R, P, M, T, V, S, or A; if said residue of said epitope is R, said semi-conservative amino acid of said analog is E, N, M, D, P, W, S, T, I, L, or Y; if said residue of said epitope is S, said semi-conservative amino acid of said analog is D, C, E, H, Q, or K; if said residue of said epitope is T, said semi-conservative amino acid of said analog is D, E, G, H, Q, V, C, K, or M; if said residue of said epitope is V, said semi-conservative amino acid of said analog is P, T, F, A, C, H, Q, E, N, or S; if said residue of said epitope is W, said semi-conservative amino acid of said analog is R, I, H, V, K, Q, S, A, P, or T; and if said residue of said epitope is Y, said semi-conservative amino acid of said analog is H, M, L, T, I, C, V, P, A, N, Q, S, K or R;

(d) performing an analysis to identify analogs that render heteroclitic activity to said epitope as measured by an increased ability to elicit a T cell response, and

(e) producing a polypeptide of 9 to 20 amino acids in length comprising an analog with heteroclitic activity.

9. The method of claim 1 , wherein the increased ability of heteroclitic analogs to elicit a T cell response is tested by inducing a primary cytotoxic T lymphocyte (CTL) response from a responder cell in a primary in vitro induction system.

10. The method of claim 8 , wherein peripheral blood mononuclear cells (PBMCs) are the responder cell source of the primary CTL.

11. The method of claim 8 , wherein the increased ability of heteroclitic analogs to elicit a T cell response is tested by inducing a primary CTL response from a responder cell in a primary in vitro induction system.

12. The method of claim 11 , wherein PBMCs are the responder cell source of the primary CTL.