Enhanced influenza hemagglutinin binders
Designed polypeptides having the amino acid sequence of SEQ ID NQ: 1 are described that bind with high affinity and selectivity to the influenza hemagglutinin protein, and which can be used for treating and/or limiting an influenza infection, as well as diagnosing an influenza infection and identifying candidate compounds for treating an influenza infection.
1. An isolated polypeptide comprising the amino acid sequence of SEQ ID NO:1, wherein the polypeptide does not comprise the amino acid sequence of 1u84 (SEQ ID NO: 5).
2. The isolated polypeptide of claim 1 , comprising the amino acid sequence of SEQ ID NO:2.
3. The isolated polypeptide of claim 1 , wherein residue 46 is selected from the group consisting of R, Y, C, and W.
4. The isolated polypeptide of claim 1 , wherein residue 46 is R.
5. The isolated polypeptide of claim 1 , wherein residue 46 is R and one or more of the following is true:
(a) residue 16 is N;
(b) residue 31 is T;
(c) residue 33 is Q;
(d) residue 70 is R; and
(e) residue 71 is T.
6. The isolated polypeptide of claim 1 , wherein one or more of the following is true:
(a) residue 45 is N;
(b) residue 65 is R; and
(c) residue 66 is L.
7. The isolated polypeptide of claim 1 , comprising a polypeptide at least 90% identical to the amino acid sequence of SEQ ID NO:3 or SEQ ID NO:4.
8. The isolated polypeptide of claim 1 , wherein one or more of the following are true:
(a) residue 33 is A, C, T, or S;
(b) residue 46 is H;
(c) residue 59 is F, W, or Y; and
(d) residue 63 is P.
9. The isolated polypeptide of claim 1 , wherein one or more of the following are true:
(a) residue 33 is C, S, A, T, or V;
(b) residue 53 is a small smaller polar/charged residue;
(c) residue 55 is S, T, or A;
(d) residue 59 is L, P, or Y;
(e) residue 68 is L;
(f) residue 72 is W; and
(g) residue 73 is E.
10. The isolated polypeptide of claim 1 , wherein one or more of the following are true:
(a) residue 36 is K;
(b) residue 52 is L;
(c) residue 53 is a small polar or charged AA; and
(d) residue 59 is Y or F.
11. The isolated polypeptide of claim 1 , wherein one or more of the following are true:
(a) residue 33 is P;
(b) residue 69 is Y;
(c) residue 70 is a polar or charged AA; and
(d) residue 73 is E.
12. The isolated polypeptide of claim 1 , wherein one or more of the following are true:
(a) residue 31 is any amino acid other than a charged amino acid;
(b) residue 33 is S or T;
(c) residue 52 is L;
(d) residue 53 is a small polar or charged AA and is not R;
(e) residue 59 is V;
(f) residue 69 is a negative AA;
(g) residue 70 is any non-positively charged AA;
(h) residue 72 is a negative AA;
(i) residue 73 is a negative AA; and
(j) residue 76 is any amino acid other than R, such as a negative AA.
13. The isolated polypeptide of claim 1 , wherein one or more of the following are true:
(a) residue 46 is H;
(b) residue 53 is a small polar or charged AA;
(c) residue 63 is R; and
(d) residue 76 is a negative AA.
14. The isolated polypeptide of claim 8 , wherein all of the listed residue options are true.
15. The isolated polypeptide according to claim 1 , wherein the polypeptide comprises a tag.
16. An isolated nucleic acid encoding the polypeptide of claim 1 .
17. A recombinant expression vector comprising the nucleic acid of claim 16 , operatively linked to a suitable control sequence.
18. A recombinant host cell comprising the recombinant expression vector of claim 17 .
19. A pharmaceutical composition, comprising one or more polypeptides according to claim 1 and a pharmaceutically acceptable carrier.
20. A method for treating and/or limiting an influenza infection, comprising administering to a subject in need thereof a therapeutically effective amount of one or more polypeptides of claim 1 , salts thereof, conjugates thereof, or pharmaceutical compositions thereof, to treat and/or limit the influenza infection.
21. The method of claim 20 , wherein the therapeutically effective amount of one or more polypeptides, salts thereof, conjugates thereof, or pharmaceutical compositions thereof are administered mucosally.
22. The method of claim 21 , wherein the mucosal administration comprises intranasal administration.
23. The method of claim 20 , wherein the therapeutically effective amount of one or more polypeptides, salts thereof, conjugates thereof, or pharmaceutical compositions thereof are administered orally.
24. The method of claim 20 , wherein the subject is immune-compromised and/or is 65 years of age or older.
25. A method for diagnosing an influenza infection, or monitoring progression of an influenza infection, comprising
(a) contacting a biological sample from a subject suspected of having an influenza infection with a diagnostically effective amount of one or more polypeptides of claim 1 , under conditions suitable for binding of the polypeptide to a viral HA protein present in the sample; and
(b) detecting polypeptide-viral HA binding complexes,
where the presence of such binding complexes indicates that the subject has an influenza infection, or provides a measure progression of an influenza infection.
26. A method for identifying candidate influenza vaccines, comprising
contacting test compounds with one or more polypeptides of claim 1 under conditions suitable for polypeptide binding;
removing unbound test compounds; and
identifying those test compounds that bind to the polypeptide of the invention, wherein such test compounds are candidate influenza vaccines.
27. A method for identifying candidate compounds for treating, limiting, and/or diagnosing influenza infection, comprising
contacting an influenza HA protein with (i) test compounds and (ii) a polypeptide of claim 1 , under conditions suitable for binding of the HA protein to the polypeptide of the present invention; and
identifying those test compounds that outcompete the polypeptide for binding to the HA protein, wherein such test compounds are candidate compounds for treating, limiting, and/or diagnosing influenza infection.