Modified interferon-beta (IFN-beta) polypeptides

• US 20080003202A1
• Filed: 03/27/2007
• Published: 01/03/2008
• Est. Priority Date: 03/28/2006
• Status: Abandoned Application

• Current Assignee: Hanall Pharmaceutical Company Limited
• Original Assignee: Hanall Pharmaceutical Company Limited
• Inventors: Guyon, Thierry, Drittanti, Lila, Borrelly, Gilles, Vega, Manuel
• Application Number:
  US11/729,266
• Publication Number:
  US 20080003202A1
• Time in Patent Office: Days
• US Class Current: 424/85.6
• CPC Class Codes: A61P 19/02 for joint disorders, e.g. arthritis, arthrosis
• CPC Class Codes: A61P 29/00 Non-central analgesic, antipyretic or antiinflammatory agents, e.g. antirheumatic agents; Non-steroidal antiinflammatory drugs [NSAID]
• CPC Class Codes: A61P 31/12 Antivirals
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: C07K 14/565 IFN-beta

Abstract

Provided are modified interferon-beta polypeptides and nucleic acid molecules encoding modified interferon-beta polypeptides and formulations containing the polypeptides and/or nucleic acid molecules. The modified polypeptides exhibit increased protein stability, including increased resistance to proteases. Also provided are methods of treatment by administering modified interferon-beta polypeptides.

Claims

1. A modified IFN-β

polypeptide, comprising;

one or more amino acid modifications in an unmodified IFN-β

polypeptide, wherein;

the one or more amino acid modifications correspond to modifications selected from among Y3I, Y3H, L6I, L6V, L6H, L6A, R11D, Q18S, Q18N, Q18H, Q18T, K19N, L20I, L20V, L20H, L20A, L21I, L21V, L21T, L21Q, L21H, L21A, Q23H, Q23S, Q23T, Q23N, L24I, L24V, L24T, L24Q, L24H, L24A, E29N, K33N, D34N, D34Q, D34G, F38I, F38V, D39N, P41A, P41S, E42N, E43N, E43K, E43Q, E43H, K45D, K45N, Q48H, Q48S, Q48T, Q48N, Q49H, Q49S, Q49T, Q49N, F50I, F50V, Q51H, Q51S, Q51T, Q51N, K52D, K52N, E53N, E53R, E53Q, E53H, D54K, D54N, D54G, D54Q, L57I, L57T, L57Q, L57H, Y60I, Y60H, E61K, E61H, E61N, E61Q, M62I, M62V, M62T, M62Q, L63I, L63V, L63T, L63Q, L63H, L63A, Q64H, Q64S, Q64T, Q64N, F70I, F70V, Q72H, Q72S, Q72T, Q72N, D73N, W79H, W79S, E81K, E81N, E85N, E85K, L87I, L87V, L87H, L87A, L88I, L88V, L88T, L88Q, L88H, L88A, L98I, L98V, L98H, L98A, K99N, L102I, L102V, L102T, L102Q, L102H, L102A, E103N, E103K, E104N, E104R, K105D, K105N, L106I, L106V, L106T, L106Q, L106H, L106A, E107N, E107R, K108D, K108N, E109R, E109N, D110K, D110N, R113E, K115D, K115N, K115S, K115H, K115Q, M117I, M117V, M117T, M117Q, M117A, L122I, L122V, L122T, L122Q, L122H, L122A, K123N, R124D, R124E, Y125I, Y125H, Y126I, Y126H, Y132I, Y132H, L133I, L133V, L133T, L133Q, L133H, L133A, K134N, K136N, E137N, W143H, W143S, R147H, R147Q, E149H, E149N, E149Q, L151I, L151V, L151T, L151Q, L511H, L151A, R152D, F154V, F154I, F156I, L160I, L160V, L160T, L160Q, L160H, L160A, L164I, L164V, L164T, L164Q, L164H, L164A, and R165D in the mature IFN-β

polypeptide set forth in SEQ ID NO;

1.

2. A modified IFN-β

polypeptide of claim 1, wherein the one or more amino acid modifications correspond to modifications selected from among Y3I, Q18S, Q18N, K19N, L20I, L20V, K33N, D34N, P41A, P41S, E42N, E43N, K45D, K45N, Q48H, Q48S, Q48T, Q49H, Q49S, Q49T, F50I, F50V, Q51H, Q51S, Q51T, Q51N, K52D, K52N, E53N, D54K, D54N, D54G, L57I, Y60I, E61K, E61H, E61N, L63I, Q64H, Q64S, Q64T, F70I, F70V, Q72H, Q72S, E85N, L88I, L88V, L98I, L98V, K99N, E103N, E104N, K105D, K105N, L106I, L106V, E107N, E109N, K115D, K115N, K115S, K115H, K123N, Y125I, Y126I, Y132I, K134N, K136N, R147H, R147Q, E149H, E149N, L151I, and F154V in the mature IFN-β

polypeptide set forth in SEQ ID NO;

1.

3. The modified IFN-β

polypeptide of claim 1 that retains at least one in vivo activity of an IFN-β

polypeptide.

4. The modified IFN-β

polypeptide of claim 1 that has 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 amino acid modifications.

5. The modified IFN-β

polypeptide of claim 1, that is a mature polypeptide.

6. The modified IFN-β

polypeptide of claim 1, that is a precursor polypeptide.

7. A modified IFN-β

polypeptide of claim 1, wherein the unmodified IFN-β

polypeptide comprises the sequence of amino acids set forth in SEQ ID NO;

1 or SEQ ID NO;

3.

8. A modified IFN-β

polypeptide of claim 1, comprising;

one or more amino acid modifications in an unmodified IFN-β

polypeptide comprising the sequence of amino acids set forth in SEQ ID NO;

3, wherein;

the one or more amino acid modifications correspond to modifications selected from among Y3I, Q18S, Q18N, K19N, L20I, L20V, L21I, L21V, K33N, D34N, P41A, P41S, E42N, E43N, K45D, K45N, Q48H, Q48S, Q48T, Q49H, Q49S, Q49T, F50I, F50V, Q51H, Q51S, Q51T, Q51N, K52D, K52N, E53N, D54K, D54N, D54G, L57I, Y60I, E61K, E61H, E61N, M62I, M62V, Q64H, Q64S, Q64T, F70I, F70V, Q72H, Q72S, E85N, L88I, L88V, L98I, L98V, K99N, E103N, E104N, K105D, K105N, L106I, L106V, E107N, E109N, K115D, K115N, K115S, K115H, M117I, M117V, L122I, L122V, K123N, Y125I, Y126I, Y132I, K134N, Y136N, R147H, R147Q, E149H, E149N, L151I, L154V, and L160V in the mature IFN-β

polypeptide set forth in SEQ ID NO;

1.

9. A modified IFN-β

polypeptide of claim 1, wherein the unmodified IFN-polypeptide is an allelic or species variant of the polypeptide whose sequence is set forth in SEQ ID NO;

1.

10. The modified IFN-β

polypeptide of claim 9, wherein the allelic or species variant has 40%, 50%, 60%, 70%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to the polypeptide whose sequence is set forth in SEQ ID NO;

1 excluding the one or more amino acid modification(s).

11. A modified IFN-β

polypeptide of claim 1, comprising a sequence of amino acids set forth in any one of SEQ ID NOS;

4-68, 71-82, 84-87, 134-153, 519, 520, 534-557, 559, 560, 562-564, 566-606 and 608-650.

12. A modified IFN-β

polypeptide of claim 1, wherein only the primary sequence is modified and the polypeptide exhibits increased protein stability.

13. A modified IFN-β

polypeptide of claim 1, wherein the polypeptide;

comprises only one amino acid modification; and

exhibits increased protein stability.

14. A modified IFN-β

polypeptide of claim 1 that exhibits increased protease resistance or increased conformational stability or a combination thereof compared to the unmodified IFN-β

polypeptide and retains one or more activities of the unmodified IFN-β

polypeptide.

15. The modified IFN-β

polypeptide of claim 14 that exhibits increased protease resistance.

16. A modified IFN-β

polypeptide of claim 14 wherein;

the one or more amino acid modifications correspond to modifications selected from among Y3H, Y3I, L6I, L6V, L6H, L6A, K19N, Q18S, Q18N, Q18H, Q18T, L20I, L20V, L20H, L20A, L21I, L21V, L21T, L21Q, L21H, L21A, Q23H, Q23S, Q23T, Q23N, L24I, L24V, L24T, L24Q, L24H, L24A, K33N, E29N, D34N, D34Q, D34G, F38I, F38V, D39N, P41A, P41S, E42N, E43Q, E43H, E43N, K45N, Q48N, Q48H, Q48S, Q48T, Q49N, Q49H, Q49S, Q49T, F50I, F50V, Q51H, Q51S, Q51T, Q51N, K52N, E53N, E53Q, E53H, D54N, D54Q, D54G, L57I, L57V, L57T, L57Q, L57H, Y60I, Y60H, E61H, E61N, E61Q, M62I, M62V, M62T, M62Q, L63I, L63V, L63T, L63Q, L63H, Q64N, Q64H, Q64S, Q64T, F70I, F70V, Q72H, Q72S, Q72T, Q72N, D73N, W79H, W79S, E81N, E85N, L87I, L87V, L87H, L87A, L88I, L88V, L88T, L88Q, L88H, L88A, L98I, L98V, L98H, L98A, K99N, L102I, L102V, L102T, L102Q, L102H, L102A, E103N, E104N, K105N, L106I, L106V, L106T, L106Q, L106H, L106A, E107N, K108N, E109N, D110N, K115N, K115S, K115H, K115Q, M117I, M117V, M117T, M117Q, M117A, L122I, L122V, L122T, L122Q, L122H, L122A, K123N, Y125I, Y125H, Y126I, Y126H, Y132I, Y132H, L133I, L133V, L133T, L133Q, L133H, K134N, K136N, E137N, W143H, W143S, R147H, R147Q, E149H, E149N, E149Q, L151I, L151V, L151T, L151Q, L151H, L151A, F154I, F154V, F156I, L160I, L160V, L160T, L160Q, L160H, L160A, L164T, L164Q, L164H, L164A, L164I, and L164V in the mature IFN-β

polypeptide set forth in SEQ ID NO;

1.

17. A modified IFN-β

polypeptide of claim 14, wherein the polypeptide exhibits increased resistance to one or more proteases selected from among pepsin, trypsin, chymotrypsin, elastase, aminopeptidase, gelatinase B, gelatinase A, α

-chymotrypsin, carboxypeptidase, endoproteinase Arg-C, endoproteinase Asp-N, endoproteinase Glu-C, endoproteinase Lys-C, luminal pepsin, microvillar endopeptidase, dipeptidyl peptidase, enteropeptidase, hydrolase, NS3, factor Xa, Granzyme B, thrombin, plasmin, urokinase, tPA and PSA.

18. A modified IFN-β

polypeptide of claim 17, wherein the protease is gelatinase B and the amino acid modification is at positions containing any one or more of an amino acid selected from among Phenylalanine (F), Leucine (L), Glutamic Acid (E), Tyrosine (Y), and Glutamine (Q).

19. A modified IFN-β

polypeptide of claim 18, wherein;

the one or more amino acid modifications correspond to modifications selected from among Y3I, Y3H, L6I, L6V, L6H, L6A, Q18S, Q18N, Q18H, Q18T, L20I, L20V, L20H, L20A, L21I, L21V, L21T, L21Q, L21H, L21A, Q23H, Q23S, Q23T, Q23N, L24I, L24V, L24T, L24Q, L24H, L24A, E29N, F38I, F38V, E42N, E43N, E43Q, E43H, Q48H, Q48S, Q48T, Q48N, Q49H, Q49S, Q49T, Q49N, F50I, F50V, Q51H, Q51S, Q51T, Q51N, E53Q, E53H, E53N, L57I, L57V, L57T, L57Q, L57H, Y60H, Y60I, E61H, E61N, E61Q, L63I, L63V, L63T, L63Q, L63H, Q64H, Q64S, Q64T, Q64N, F70I, F70V, Q72H, Q72S, Q72T, Q72N, E81N, E85N, L87I, L87V, L87H, L87A, L88I, L88V, L88T, L88Q, L88H, L88A, L98I, L98V, L98H, L98A, L102I, L102V, L102T, L102Q, L102H, L102A, E103N, E104N, L106I, L106V, L106T, L106Q, L106H, L106A, E107N, E109N, Y125I, Y125H, Y126I, Y126H, Y132I, Y132H, L133I, L133V, L133T, L133Q, L133H, E137N, E149H, E149N, E149Q, L151I, L151V, L151T, L151Q, L151H, L151A, F154I, F154V, F156I, L160I, L160V, L160T, L160Q, L160H, L160A, L164I, L164V, L164H, L164A, L164T, and L164Q in the mature IFN-β

polypeptide set forth in SEQ ID NO;

1.

20. A modified IFN-β

polypeptide of claim 14 that exhibits increased conformational stability, wherein;

the one or more amino acid modifications correspond to modifications selected from among R11D, E43K, K45D, K52D, E53R, D54K, E61K, E81K, E85K, E103K, E104R, K105D, E107R, E109R, D110K, R113E, K115Q, K15D, R124D, R124E, R152D, and R165D.

21. A modified IFN-β

polypeptide of claim 14, wherein;

the one or more amino acid modifications increase the isoelectric point of the polypeptide; and

the amino acid modification is replacement by one or more amino acid residues selected from among a Glutamic Acid (E) or an Aspartic Acid (D) to a Lysine (K) or to an Arginine (R);

or

the one or more amino acid modifications decrease the isoelectric point of the polypeptide; and

the one or more amino acid modification(s) is replacement by one or more amino acid residues selected from among a Lysine (K) or an Arginine (R) to a Glutamine (Q), to a Glutamic Acid (E) or to an Aspartic Acid (D).

22. A modified IFN-β

polypeptide of claim 21 wherein;

the one or more amino acid modifications increase the isoelectric point; and

the one or more amino acid modifications correspond to modifications selected from among E43K, E53R, D54K, E61K, E81K, E85K, E103K, E104R, E107R, E109R, and D110K in the mature IFN-β

polypeptide set forth in SEQ ID NO;

1.

23. A modified IFN-β

polypeptide of claim 21, wherein;

the one or more amino acid modifications decrease the isoelectric point; and

the one or more amino acid modifications correspond to modifications selected from among K115Q, R11D, K45D, K52D, K105D, K108D, R113E, K115D, R124D, R124E, R152D, and R165D in the mature IFN-β

polypeptide set forth in SEQ ID NO;

1.

24. A modified IFN-β

polypeptide of claim 1, comprising one or more further amino acid modification(s) at one or more positions corresponding to amino acid positions selected from among M1, Y3, L5, L6, F8, L9, Q10, R11, S12, S13, N14, F15, Q16, C17, Q18, K19, L20, L21, W22, Q23, L24, N25, R27, L28, E29, Y30, L32, K33, D34, R35, M36, F38, D39, E42, E43, K45, L47, Q48, Q49, K52, E53, D54, L57, Y60, E61, M62, L63, Q64, F67, R71, Q72, D73, G78, W79, N80, E81, T82, I83, E85, N86, L87, L88, A89, N90, V91, Y92, Q94, I95, H97, L98, K99, V101, L102, E103, E104, K105, L106, E107, K108, E109, D110, F111, R113, K115, L116, M117, L120, L122, K123, R124, Y125, Y126, R128, L130, Y132, L133, K134, N136, E137, Y138, W143, E149, L151, R152, F154, Y155, F156, R159, L160, Y163, L164, and R165 in the mature IFN-β

polypeptide set forth in SEQ ID NO;

1.

25. A modified IFN-β

polypeptide of claim 24, wherein the one or more further amino acid modification(s) correspond to modifications selected from among M1C, M1D, M1E, M1K, M1N, M1R, M1S, M1V, M1I, M1T, M1A, M1Q, Y3H, L5V, L5I, L5T, L5Q, L5H, L5A, L5D, L5E, L5K, L5R, L5N, L5S, L6I, L6V, L6H, L6A, L6D, L6E, L6K, L6N, L6Q, L6R, L6S, L6T, L6C, F8I, F8V, F8D, F8E, F8K, F8R, L9V, L9I, L9T, L9Q, L9H, L9A, L9D, L9E, L9K, L9N, L9R, L9S, Q10D, Q10E, Q10K, Q10N, Q10R, Q10S, Q10T, Q10C, R11D, R11H, R11Q, S12D, S12E, S12K, S12R, S13D, S13E, S13K, S13N, S13Q, S13R, S13T, S13C, N14D, N14E, N14K, N14Q, N14R, N14S, N14T, F15D, F15E, F15K, F15R, F15I, F15V, Q16D, Q16E, Q16K, Q16N, Q16R, Q16S, Q16C, Q16T, C17D, C17E, C17K, C17N, C17Q, C17R, C17S, C17T, Q18H, Q18T, K19Q, K19T, K19S, K19H, L20H, L20A, L20N, L20Q, L20R, L20S, L20T, L20D, L20E, L20K, L21I, L21V, L21T, L21Q, L21H, L21A, W22D, W22E, W22K, W22R, W22S, W22H, Q23H, Q23S, Q23T, Q23N, Q23D, Q23E, Q23K, Q23R, L24I, L24V, L24T, L24Q, L24H, L24A, L24D, L24E, L24K, L24R, N25H, N25S, N25Q, R27H, R27Q, L28V, L28I, L28T, L28Q, L28H, L28A, E29N, E29Q, E29H, Y30H, Y30I, L32V, L32I, L32T, L32Q, L32H, L32A, K33Q, K33T, K33S, K33H, D34Q, D34G, R35H, R35Q, M36V, M36I, M36T, M36Q, M36A, F38I, F38V, D39N, D39Q, D39H, D39G, E42Q, E42H, E43K, E43Q, E43H, K45Q, K45T, K45S, K45H, L47V, L47I, L47T, L47Q, L47H, L47A, Q48N, Q49N, K52Q, K52T, K52S, K52H, E53R, E53Q, E53H, D54Q, L57V, L57T, L57Q, L57H, L57A, Y60H, E61Q, M62I, M62V, M62T, M62Q, M62A, L63V, L63T, L63Q, L63H, L63A, Q64N, F67I, F67V, R71H, R71Q, Q72N, D73N, D73H, D73G, D73Q, G78D, G78E, G78K, G78R, W79H, W79S, W79D, W79E, W79K, W79R, N80D, N80E, N80K, N80R, E81K, E81N, E81Q, E81H, T82D, T82E, T82K, T82R, I83D, I83E, I83K, I83R, I83N, I83Q, I83S, I83T, E85K, E85Q, E85H, N86D, N86E, N86K, N86R, N86Q, N86S, N86T, L87I, L87V, L87H, L87A, L87D, L87E, L87K, L87R, L87N, L87Q, L87S, L87T, L88T, L88Q, L88H, L88A, A89D, A89E, A89K, A89R, N90D, N90E, N90K, N90Q, N90R, N90S, N90T, N90C, V91D, V91E, V91K, V91N, V91Q, V91R, V91S, V91T, V91C, Y92H, Y92I, Q94D, Q94E, Q94K, Q94N, Q94R, Q94S, Q94T, Q94C, I95D, I95E, I95K, I95N, I95Q, I95R, I95S, I95T, H97D, H97E, H97K, H97N, H97Q, H97R, H97S, H97T, H97C, L98H, L98A, L98D, L98E, L98K, L98N, L98Q, L98R, L98S, L98T, L98C, K99Q, K99T, K99S, K99H, V101D, V101E, V101K, V101N, V101Q, V101R, V101S, V101T, V101C, L102I, L102V, L102T, L102Q, L102H, L102A, E103K, E103Q, E103H, E104R, E104Q, E104H, K105Q, K105T, K105S, K105H, L106T, L106Q, L106H, L106A, E107R, E107Q, E107H, K108D, K108N, K108Q, K108T, K108S, K108H, E109R, E109Q, E109H, D110K, D110N, D110Q, D110H, D110G, F111I, F111V, R113E, R113H, R113Q, K115Q, L116V, L116I, L116T, L116Q, L116H, L116A, M117I, M117V, M117T, M117Q, M117Q, M117A, L120V, L120I, L120T, L120Q, L120H, L120A, L122I, L122V, L122T, L122Q, L122H, L122A, K123Q, K123T, K123S, K123H, R124D, R124E, R124H, R124Q, Y125H, Y126H, R128H, R128Q, L130V, L130I, L130T, L130Q, L130H, L130A, Y132H, L133I, L133V, L133T, L133Q, L133H, L133A, K134Q, K134T, K134S, K134H, K136Q, K136T, K136S, K136H, E137N, E137Q, E137H, Y138H, Y138I, W143H, W143S, E149Q, L151V, L151T, L151Q, L151H, L151A, R152D, R152H, R152Q, F154I, Y155H, Y155I, F156I, F156V, R159H, R159Q, L160I, L160V, L160T, L160Q, L160H, L160A, Y163H, Y163I, L164I, L164V, L164T, L164Q, L164H, L164A, R165D, R165Q and R165H in the mature IFN-β

polypeptide set forth in SEQ ID NO;

1.

26. A modified IFN-β

polypeptide of claim 24, wherein the one or more further amino acid modification(s) at one or more positions corresponding to amino acid positions is selected from among M1, Y3, L5, L6, F8, L9, Q10, R11, S12, S13, N14, F15, Q16, C17, Q18, K19, L20, L21, W22, Q23, L24, N25, R27, L28, E29, Y30, L32, K33, D34, R35, M36, F38, D39, E42, E43, K45, L47, Q48, Q49, K52, E53, D54, L57, Y60, E61, M62, L63, Q64, F67, R71, Q72, D73, G78, W79, N80, E81, T82, I83, E85, N86, L87, L88, A89, N90, V91, Y92, Q94, I95, H97, L98, K99, V101, L102, E103, E104, K105, L106, E107, K108, E109, D110, F111, R113, K115, L116, M117, L122, K123, R124, Y125, Y126, R128, L130, Y132, L133, K134, K136, E137, Y138, W143, E149, L151, R152, Y155, F156, R159, L160, Y163, L164, and R165 in the mature IFN-β

polypeptide set forth in SEQ ID NO;

1; and

the modified IFN-β

polypeptide exhibits increased protease resistance compared to an IFN-β

polypeptide that does not include the modification(s).

27. A modified IFN-β

polypeptide of claim 26, wherein the one or more further amino acid modification(s) correspond to modifications selected from among M1V, M1I, M1T, M1A, M1Q, M1D, M1E, M1K, M1N, M1R, M1S, M1C, Y3H, L5V, L5I, L5T, L5Q, L5H, L5A, L5D, L5E, L5K, L5R, L5N, L5S, L6H, L6A, L6I, L6V, L6D, L6E, L6K, L6N, L6Q, L6R, L6S, L6T, L6T, L6C, F8I, F8V, F8D, F8E, F8K, F8R, L9V, L9I, L9T, L9Q, L9H, L9A, L9D, L9E, L9K, L9N, L9R, L9S, Q10D, Q10E, Q10K, Q10N, Q10R, Q10S, Q10T, Q10C, R11H, R11Q, S12D, S12E, S12K, S12R, S13D, S13E, S13K, S13N, S13Q, S13R, S13T, S13C, N14D, N14E, N14K, N14Q, N14R, N14S, N14T, F15I, F15V, F15D, F15E, F15K, F15R, Q16D, Q16E, Q16K, Q16N, Q16R, Q16S, Q16T, Q16C, C17D, C17E, C17K, C17N, C17R, C17S, C17T, Q18H, Q18T, K19Q, K19T, K19S, K19H, L20H, L20A, L20N, L20Q, L20R, L20S, L20T, L20D, L20E, L20K, L21I, L21V, L21T, L21Q, L21H, L21A, W22S, W22H, W22D, W22E, W22K, W22R, Q23H, Q23S, Q23T, Q23N, Q23D, Q23E, Q23K, Q23R, L24T, L24Q, L24H, L24I, L24V, L24D, L24E, L24K, L24R, N25H, N25S, N25Q, R27H, R27Q, L28V, L28I, L28T, L28Q, L28H, L28A, E29N, E29Q, E29H, Y30H, Y30I, L32V, L32I, L32T, L32Q, L32H, L32A, K33Q, K33T, K33S, K33H, D34Q, D34G, R35H, R35Q, M36V, M36I, M36T, M36Q, M36A, F38I, F38V, D39N, D39Q, D39H, D39G, E42Q, E42H, E43Q, E43H, K45Q, K45T, K45S, K45T, L47V, L47I, L47T, L47Q, L47H, L47A, Q48N, Q49N, K52Q, K52T, K52S, K52H, E53Q, E53H, D54Q, L57T, L57Q, L57H, L57A, L57V, Y60H, E61Q, M62I, M62V, M62T, M62Q, M62A, L63T, L63Q, L63H, L63A, L63V, Q64N, F67I, F67V, R71H, R71Q, Q72T, Q72N, D73N, D73Q, D73H, D73G, G78D, G78E, G78K, G78R, W79H, W79S, N80D, N80E, N80K, N80R, E81N, E81Q, E81H, T82D, T82E, T82K, T82R, I83D, I83E, I83K, I83R, I83N, I83Q, I83S, I83T, E85 Q, E85H, N86D, N86E, N86K, N86R, N86Q, N86S, N86T, L87H, L87A, L88T, L88Q, L88H, L88A, L87I, L87V, L87D, L87E, L87K, L87R, L87N, L87Q, L87S, L87T, A89D, A89E, A89K, A89R, N90D, N90E, N90K, N90Q, N90R, N90S, N90T, N90C, V91D, V91E, V91K, V91N, V91Q, V91R, V91S, V91T, V91C, Y92H, Y92I, Q94D, Q94E, Q94K, Q94N, Q94R, Q94S, Q94T, Q94C, I95D, I95E, I95K, I95N, I95Q, I95R, I95S, I95T, H97D, H97E, H97K, H97N, H97Q, H97R, H97S, H97T, H97C, L98H, L98A, L98D, L98E, L98K, L98N, L98Q, L98R, L98S, L98T, L98C, K99Q, K99T, K99S, K99H, V101D, V101E, V101K, V101N, V101Q, V101R, V101S, V101T, V101C, L102T, L102Q, L102H, L102A, L102I, L102V, E103Q, E103H, E104Q, E104H, K105Q, K105T, K105S, K105H, L106T, L106Q, L106H, L106A, E107H, K108N, K108Q, K108T, K108S, K108H, E109H, E109Q, D110N, D100Q, D110H, D110G, F111I, F111V, R113H, R113Q, K115Q, L116V, L116I, L116T, L116Q, L116H, L116A, M117I, M117V, M117T, M117Q, M117A, L122I, L122V, L122T, L122Q, L122H, L122A, K123Q, K123T, K123S, K123H, R124H, R124Q, Y125H, Y126H, R128H, R128Q, L130V, L130I, L130T, L130Q, L130H, L130A, L133T, L133Q, L133H, L133A, Y132I, K134Q, K134T, K134S, K134H, K136Q, K136T, K136S, K136H, E137N, E137Q, E137H, Y138H, Y138I, W143H, W143S, E149Q, L151T, L151Q, L151H, L151A, L151V, R152H, R152Q, F154V, F154I, Y155H, Y155I, F156I, F156V, R159H, R159Q, L160V, L160T, L160Q, L160H, L160A, L160I, Y163H, Y163I, L164T, L164Q, L164H, L164A, L164I, L164V, R165H, and R165Q in the mature IFN-β

polypeptide set forth in SEQ ID NO;

1.

28. A modified IFN-β

polypeptide of claim 24, wherein the one or more further amino acid modification(s) at one or more positions corresponding to amino acid positions is selected from among Y3, L5, L6, F8, L9, Q10, F15, Q16, Q18, L20, L21, Q23, L28, E29, Y30, L32, F38, E42, E43, L47, Q48, Q49, E53, L57, Y60, E61, L63, Q64, F67, Q72, E81, E85, L87, L88, Y92, Q94, L98, L102, E103, E104, L106, E107, E109, F111, L116, L120, Y125, Y126, L130, Y132, L133, E137, Y138, E149, L151, F154, F156, L160, Y163, and L164 in the mature IFN-β

polypeptide set forth in SEQ ID NO;

1; and

the modified IFN-β

polypeptide exhibits increased resistance to gelatinase B proteolysis compared to an IFN-β

polypeptide that does not include the modification(s).

29. A modified IFN-β

polypeptide of claim 28, wherein the one or more further amino acid modification(s) correspond to modifications selected from among Y3H, L5V, L5I, L5T, L5Q, L5H, L5A, L5D, L5E, L5K, L5R, L5N, L5S, L6I, L6V, L6H, L6A, L6D, L6E, L6K, L6N, L6Q, L6R, L6S, L6T, L6C, F8I, F8V, F8D, F8E, F8K, F8R, L9V, L9I, L9T, L9Q, L9H, L9A, L9D, L9E, L9K, L9N, L9R, L9S, Q10D, Q10E, Q10K, Q10N, Q10R, Q10S, Q10T, Q10C, F15I, F15V, F15D, F15E, F15K, F15R, Q16D, Q16E, Q16K, Q16N, Q16R, Q16S, Q16T, Q16C, Q18H, Q18T, L20H, L20A, L20N, L20Q, L20R, L20S, L20T, L20D, L20E, L20K, L21I, L21V, L21T, L21Q, L21H, L21A, Q23H, Q23S, Q23T, Q23N, Q23D, Q23E, Q23K, Q23R, L28V, L28I, L28T, L28Q, L28H, L28A, E29N, E29Q, E29H, Y30H, Y30I, L32V, L32I, L32T, L32Q, L32H, L32A, F38I, F38V, E42Q, E42H, E43Q, E43H, L47V, L47I, L47T, L47Q, L47H, L47A, Q48N, Q49N, E53Q, E53H, L57V, L57T, L57Q, L57H, L57A, Y60H, E61Q, L63V, L63T, L63Q, L63H, L63A, Q64N, F67I, F67V, Q72T, Q72N, E81N, E81Q, E81H, E85Q, E85H, L87I, L87V, L87H, L87A, L87D, L87E, L87, L87R, L87N, L87Q, L87S, L87T, L88T, L88Q, L88H, L88A, Y92H, Y92I, Q94D, Q94E, Q94K, Q94N, Q94R, Q94S, Q94T, Q94C, L98H, L98A, L98D, L98E, L98K, L98N, L98Q, L98R, L98S, L98T, L98C, L102I, L102V, L102T, L102Q, L102H, L102A, E103Q, E103H, E104Q, E104H, L106T, L106Q, L106H, L106A, E107Q, E107H, E109H, E109Q, F111I, F111V, L116V, L116I, L116T, L116Q, L116H, L116A, L116V, L116I, L116T, L116Q, L116H, L116A, Y125H, Y126H, L130V, L130I, L130T, L130Q, L130H, L130A, Y132H, L133I, L133V, L133T, L133Q, L133H, L133A, E137N, E137Q, E137H, Y138H, Y138I, E149Q, L151V, L151T, L151Q, L151H, L151A, F154I, F156I, F156V, L160I, L160V, L160T, L160Q, L160H, L160A, Y163H, Y163I, L164I, L164V, L164T, L164Q, L164H, and L164A in the mature IFN-β

polypeptide set forth in SEQ ID NO;

1.

30. A modified IFN-β

polypeptide of claim 24, wherein the one or more further amino acid modification(s) is at one or more positions corresponding to amino acid positions is selected from among R11, K45, K52, K105, K108, R113, K115Q, R124, R152, and R165 in the mature IFN-β

polypeptide set forth in SEQ ID NO;

1; and

the modified IFN-β

polypeptide exhibits a decreased isoelectric point compared to an IFN-β

polypeptide that does not include the modification(s).

31. A modified IFN-β

polypeptide of claim 30, wherein the one or more further amino acid modification(s) correspond to modifications selected from among R11Q, R11D, K45Q, K52Q, K105Q, K108Q, K108D, R113Q, R113E, K115Q, R124Q, R124D, R124E, R152Q, R152D, R165Q, and R165D in the mature IFN-β

polypeptide set forth in SEQ ID NO;

1.

32. A modified IFN-β

polypeptide of claim 1, further comprising one or more amino acid modifications contributing to one or more of deimmunization, glycosylation, and/or PEGylation of the polypeptide.

33. A modified IFN-β

polypeptide of claim 32, wherein the polypeptide is glycosylated and/or conjugated to a polyethylene glycol (PEG) moiety.

66. A modified IFN-β

polypeptide of any of claims 1, 34 and 49, wherein the one or more amino acid modifications are selected from natural amino acids, non-natural amino acids and a combination of natural and non-natural amino acids.

67. The modified IFN-β

polypeptide of any of claims 1, 34 and 49 that is a naked polypeptide chain.

68. The modified IFN-β

polypeptide of any of claims 1, 34 and 49 that is pegylated, albuminated and/or glycosylated.

69. A nucleic acid molecule, comprising a sequence of nucleotides encoding a modified IFN-β

polypeptide of any of claims 1, 34 and 49.

70. A vector, comprising the nucleic acid molecule of claim 69.

71. A cell, comprising the vector of claim 70.

72. The cell of claim 71 that is a eukaryotic cell.

73. The cell of claim 71 that is a prokaryotic cell.

74. A method for production of a modified IFN-β

polypeptide, comprising introducing a nucleic acid molecule of claim 69 into a cell, and culturing the cell under conditions whereby the encoded modified IFN-β

polypeptide is expressed.

75. A method for production of a modified IFN-β

polypeptide, comprising introducing a nucleic acid molecule of claim 69 into a cell-free system, whereby the encoded modified IFN-β

polypeptide is expressed.

76. The method of claim 74, wherein the modified IFN-β

polypeptide is glycosylated.

77. A pharmaceutical composition, comprising a modified IFN-β

polypeptide of any of claims 1, 34 and 49 in a pharmaceutically acceptable excipient.

78. A pharmaceutical composition, consisting essentially of a modified IFN-β

polypeptide of any of claims 1, 34 and 49.

79. The pharmaceutical composition of claim 77 that is formulated for oral, nasal or pulmonary administration.

80. The pharmaceutical composition of claim 79, wherein:

the IFN-β

polypeptide exhibits increased protease resistance; and

the composition that is formulated for oral administration.

81. The pharmaceutical composition of claim 80, where the polypeptide exhibits increased resistance to one or more proteases selected from among pepsin, trypsin, chymotrypsin, elastase, aminopeptidase, gelatinase B, gelatinase A, α

-chymotrypsin, carboxypeptidase, endoproteinase Arg-C, endoproteinase Asp-N, endoproteinase Glu-C, endoproteinase Lys-C, luminal pepsin, microvillar endopeptidase, dipeptidyl peptidase, enteropeptidase, hydrolase, NS3, factor Xa, Granzyme B, thrombin, plasmin, urokinase, tPA and PSA.

82. The pharmaceutical composition of claim 77, wherein the pharmaceutical composition does not contain exogenously added protease inhibitors.

83. The pharmaceutical composition of claim 77 that is formulated as a liquid, a pill, a tablet, a lozenge or a capsule.

84. The pharmaceutical composition of claim 83, wherein the lozenge delivers the modified IFN-β

polypeptide to the mucosa of the mouth, throat, or gastrointestinal tract.

85. The pharmaceutical composition of claim 77, wherein the pharmaceutical composition is formulated for controlled-release of the modified IFN-β

polypeptide.

86. The pharmaceutical composition of claim 83, wherein the pill, tablet, or capsule is coated with an enteric coating.

87. A method, comprising treating a subject by administering the pharmaceutical composition of claim 77, wherein the subject has a disease or condition that is responsive to administration of IFN-β

.

88. The method of claim 87, wherein the disease or condition is selected from among a viral infection, a proliferative disorder, an autoimmune disease, and an inflammatory disorder.

89. The method of claim 88, wherein the autoimmune disease is multiple sclerosis, rheumatoid arthritis, chronic viral hepatitis, hepatitis A, hepatitis B, and myocardial viral infection.

90. The method of claim 88, wherein the proliferative disease is a cancer or bone disorder.

91. The method of claim 90, wherein the cancer is selected from among uveal melanoma, colon cancer, liver cancer, and a metastatic cancer.

92. The method of claim 90, wherein the bone disorder is osteoporosis or osteopenia.

93. The method of claim 88, wherein the inflammatory disorder is selected from among asthma, Guillain-Barre syndrome, and an inflammatory bowel disease.

94. The method of claim 93, wherein the inflammatory bowel disease is ulcerative colitis or Crohn'"'"'s disease.

95. The method of claim 88, wherein the viral infection is chronic viral hepatitis or myocardial viral infection.

34. A modified IFN-β

polypeptide, comprising;

two or more amino acid modifications in an unmodified IFN-β

polypeptide, wherein;

the two or more amino acid modifications are at two or more positions corresponding to amino acid positions selected from among Y3, L6, R11, Q18, K19, L20, L21, Q23, L24, E29, K33, D34, F38, D39, P41, E42, E43, K45, Q48, Q49, F50, Q51, K52, E53, D54, L57, Y60, E61, M62, L63, Q64, F70, Q72, D73, W79, E81, E85, L87, L88, L98, K99, L102, E103, E104, K105, L106, E107, K108, E109, D110, R113, K115, M117, L122, K123, R124, Y125, Y126, Y132, L133, K134, K136, E137, W143, R147, E149, L151, R152, F154, F156, L160, L164, and R165 in the mature IFN-β

polypeptide set forth in SEQ ID NO;

1.

35. The modified IFN-β

polypeptide of claim 34 that retains at least one in vivo activity of an IFN-β

polypeptide.

36. The modified IFN-β

polypeptide of claim 34 that has 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 amino acid modifications.

37. The modified IFN-β

polypeptide of claim 34 that is a mature polypeptide.

38. The modified IFN-β

polypeptide of claim 34 that is a precursor polypeptide.

39. A modified IFN-β

polypeptide of claim 34, wherein the two or more amino acid modification(s) correspond to modifications selected from among Y3I, Y3H, L6I, L6V, L6H, L6A, R11D, Q18H, Q18S, Q18T, Q18N, K19N, L20I, L20V, L20H, L20A, L21I, L21V, L21T, L21Q, L21H, L21A, Q23H, Q23S, Q23T, Q23N, L24I, L24V, L24T, L24Q, L24H, L24A, E29N, K33N, D34N, D34Q, D34G, F38I, F38V, D39N, P41A, P41S, E42N, E43K, E43Q, E43H, E43N, K45D, K45N, Q48H, Q48S, Q48T, Q48N, Q49H, Q49S, Q49T, Q49N, F50I, F50V, Q51H, Q51S, Q51T, Q51N, K52D, K52N, E53R, E53Q, E53H, E53N, D54G, L57I, L57V, L57T, L57Q, L57H, L57A, Y60H, Y60I, E61K, E61Q, E61H, E61N, M62I, M62V, M62T, M62Q, M62H, M62A, L63I, L63V, L63T, L63Q, L63H, L63A, Q64H, Q64S, Q64T, Q64N, F70I, F70V, Q72H, Q72S, Q72T, Q72N, D73N, W79H, W79S, E81K, E81N, E85K, E85N, L87I, L87V, L87H, L87A, L88I, L88V, L88T, L88Q, L88H, L88A, L98I, L98V, L98H, L98A, K99N, L102I, L102V, L102T, L102Q, L102H, L102A, E103K, E103N, E104R, E104N, K105D, K105N, L106I, L106V, L106T, L106Q, L106H, L106A, E107R, E107N, K108D, K108N, E109R, E109N, D110K, D110N, R113E, K115D, K115Q, K115N, K115S, K115H, M117I, M117V, M117T, M117Q, M117A, L122I, L122V, L122T, L122Q, L122H, L122A, K123N, R124D, R124E, Y125H, Y125I, Y126H, Y126I, Y132H, Y132I, L133I, L133V, L133T, L133Q, L133H, L133A, K134N, K136N, E137N, W143H, W143S, R147H, R147Q, E149Q, E149H, E149N, L151I, L151V, L151T, L151Q, L151H, L151A, R152D, F154I, F154V, F156I, F156V, L160I, L160V, L160T, L160Q, L160H, L160A, L164I, L164V, L164T, L164Q, L164H, L164A, R165D in the mature IFN-β

polypeptide set forth in SEQ ID NO;

1.

40. The modified IFN-β

polypeptide of claim 34, wherein the unmodified IFN-β

polypeptide contains a sequence of amino acids set forth in SEQ ID NOS;

1 or 3.

41. The modified IFN-β

polypeptide of claim 34, wherein the unmodified IFN-β

polypeptide is an allelic or species variant of the polypeptide set forth in SEQ ID NO;

1.

42. The modified IFN-β

polypeptide of claim 41, wherein the allelic or species variant has 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to the polypeptide set forth in SEQ ID NO;

1 excluding the amino acid modification(s).

43. The modified IFN-β

polypeptide of claim 34, wherein only the primary sequence is modified and the polypeptide exhibits increased protein stability.

44. The modified IFN-β

polypeptide of claim 34 that exhibits increased protease resistance compared to the unmodified IFN-β

polypeptide and retains one or more activities of the unmodified IFN-β

polypeptide

45. A modified IFN-β

polypeptide of claim 34, comprising one or more further amino acid modifications at one or more positions corresponding to amino acid positions selected from among M1, L5, L6, F8, L9, Q10, R11, S12, S13, N14, F15, Q16, C17, K19, L20, W22, Q23, L24, N25, R27, L28, E29, Y30, L32, K33, R35, M36, D39, E42, K45, L47, K52, F67, R71, D73, G78, W79, N80, E81, T82, I83, E85, N86, L87, A89, N90, V91, Y92, Q94, I95, H97, L98, K99, V101, E103, E104, K105, E107, K108, E109, D110, F111, R113, L116, L120, K123, R124, R128, L130, K134, K136, E137, Y138, R152, Y155, R159, Y163, and R165 in the mature IFN-β

polypeptide set forth in SEQ ID NO;

1.

46. A modified IFN-β

polypeptide of claim 45, wherein the one or more further amino acid modification(s) correspond to modifications selected from among M1V, M1I, M1T, M1A, M1Q, M1D, M1E, M1K, M1N, M1R, M1S, M1C, L5V, L5I, L5T, L5Q, L5H, L5A, L5D, L5E, L5K, L5R, L5N, L5S, L6D, L6E, L6K, L6N, L6Q, L6R, L6S, L6T, L6T, L6C, F8I, F8V, F8D, F8E, F8K, F8R, L9V, L9I, L9T, L9Q, L9H, L9A, L9D, L9E, L9K, L9N, L9R, L9S, Q10D, Q10E, Q10K, Q10N, Q10R, Q10S, Q10T, Q10C, R11H, R11Q, S12D, S12E, S12K, S12R, S13D, S13E, S13K, S13N, S13Q, S13R, S13T, S13C, N14D, N14E, N14K, N14Q, N14R, N14S, N14T, F15I, F15V, F15D, F15E, F15K, F15R, Q16D, Q16E, Q16K, Q16N, Q16R, Q16S, Q16T, Q16C, C17D, C17E, C17K, C17N, C17R, C17S, C17T, K19Q, K19T, K19S, K19H, L20N, L20Q, L20R, L20S, L20T, L20D, L20E, L20K, W22S, W22H, W22D, W22E, W22K, W22R, Q23D, Q23E, Q23K, Q23R, L24D, L24E, L24K, L24R, N25H, N25S, N25Q, R27H, R27Q, L28V, L28I, L28T, L28Q, L28H, L28A, E29Q, E29H, Y30H, Y30I, L32V, L32I, L32T, L32Q, L32H, L32A, K33Q, K33T, K33S, K33H, R35H, R35Q, M36V, M36I, M36T, M36Q, M36A, D39Q, D39H, D39G, E42Q, E42H, K45Q, K45T, K45S, K45T, L47V, L47I, L47T, L47Q, L47H, L47A, K52Q, K52T, K52S, K52H, F67I, F67V, R71H, R71Q, D73Q, D73H, D73G, G78D, G78E, G78K, G78R, N80D, N80E, N80K, N80R, E81Q, E81H, T82D, T82E, T82K, T82R, I83D, I83E, I83K, I83R, I83N, I83Q, I83S, I83T, E85Q, E85H, N86D, N86E, N86K, N86R, N86Q, N86S, N86T, L87D, L87E, L87K, L87R, L87N, L87Q, L87S, L87T, A89D, A89E, A89K, A89R, N90D, N90E, N90K, N90Q, N90R, N90S, N90T, N90C, V91D, V91E, V91K, V91N, V91Q, V91R, V91S, V91T, V91C, Y92H, Y92I, Q94D, Q94E, Q94K, Q94N, Q94R, Q94S, Q94T, Q94C, I95D, I95E, I95K, I95N, I95Q, I95R, I95S, I95T, H97D, H97E, H97K, H97N, H97Q, H97R, H97S, H97T, H97C, L98D, L98E, L98K, L98N, L98Q, L98R, L98S, L98T, L98C, K99Q, K99T, K99S, K99H, V101D, V101E, V101K, V101N, V101Q, V101R, V101S, V101T, V101C, E103Q, E103H, E104Q, E104H, K105Q, K105T, K105S, K105H, E107Q, E107H, K108Q, K108T, K108S, K108H, E109H, E109Q, D110Q, D110H, D110G, F111I, F111V, R113H, R113Q, L116V, L116I, L116T, L116Q, L116H, L116A, L120V, L120I, L120T, L120Q, L120H, L120A, K123Q, K123T, K123S, K123H, R124H, R124Q, R128H, R128Q, L130V, L130I, L130T, L130Q, L130H, L130A, K134Q, K134T, K134S, K134H, K136Q, K136T, K136S, K136H, E137Q, E137H, Y138H, Y138I, R152H, R152Q, Y155H, Y155I, R159H, R159Q, Y163H, Y163I, R165H, and R165Q in the mature IFN-β

polypeptide.

47. A modified IFN-β

polypeptide of claim 34, further-comprising one or more amino acid modifications contributing to one or more of deimmunization, glycosylation and PEGylation of the polypeptide.

48. A modified IFN-β

polypeptide of claim 47, wherein the polypeptide is glycosylated or conjugated to a polyethylene glycol (PEG) moiety.

49. A modified IFN-β

polypeptide, comprising;

two or more amino acid modifications in an unmodified IFN-β

polypeptide, wherein;

the two or more amino acid modifications are at two or more positions corresponding to amino acid positions selected from among M1, L5, L6, F8, L9, Q10, R11, S12, S13, N14, F15, Q16, C17, L20, W22, Q23, L24, E43, K45, K52, E53, D54, E61, G78, W79, N80, E81, T82, I83, E85, N86, L87, A89, N90, V91, Q94, I95, H97, L98, V101, E103, E104, K105, E107, K108, E109, D110, R113, K115, R124, R152, and R165 in the mature IFN-β

polypeptide set forth in SEQ ID NO;

1;

the modified IFN-β

polypeptide exhibits increased protein stability manifested as increased conformational stability compared to the unmodified IFN-β

polypeptide; and

the modified IFN-β

polypeptide retains one or more activities of the unmodified IFN-β

polypeptide.

50. The modified IFN-β

polypeptide of claim 49 that has 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 amino acid modifications.

51. A modified IFN-β

polypeptide of claim 49 that is a mature IFN-β

polypeptide.

52. A modified IFN-β

polypeptide of claim 49 that is a precursor IFN-β

polypeptide.

53. A modified IFN-β

polypeptide of claim 49, wherein the two or more amino acid modification(s) correspond to modifications selected from among M1E, M1D, M1K, M1R, M1N, M1Q, M1S, M1T, M1C, L5E, L5D, L5K, L5R, L5N, L5Q, L5S, L5T, L6C, F8E, F8D, F8K, F8R, L9E, L9D, L9K, L9R, L9N, L9Q, L9S, L9T, Q10C, Q10E, Q10D, Q10K, Q10R, Q10N, Q10S, Q10T, R11Q, R11D, S12E, S12D, S12K, S12R, S13E, S13D, S13K, S13R, S13N, S13Q, S13T, S13C, N14E, N14D, N14K, N14R, N14Q, N14S, N14T, F15E, F15D, F15K, F15R, Q16E, Q16D, Q16K, Q16R, Q16N, Q16S, Q16T, Q16C, C17E, C17D, C17K, C17R, C17N, C17Q, C17S, C17T, L20E, L20D, L20K, L20R, L20N, L20Q, L20S, L20T, W22E, W22D, W22K, W22R, Q23E, Q23D, Q23K, Q23R, L24E, L24D, L24K, L24R, E43K, K45Q, K45D, K52Q, K52D, E53R, D54K, E61K, G78E, G78D, G78K, G78R, W79E, W79D, W79K, W79R, N80E, N80D, N80K, N80R, E81K, T82E, T82D, T82K, T82R, I83E, I83D, I83K, I83R, I83N, I83Q, I83S, I83T, E85K, N86E, N86D, N86K, N86R, N86Q, N86S, N86T, L87E, L87D, L87K, L87R, L87N, L87Q, L87S, L87T, A89E, A89D, A89K, A89R, N90E, N90D, N90K, N90R, N90Q, N90S, N90T, N90C, V91E, V91D, V91K, V91R, V91N, V91Q, V91S, V91T, V91C, Q94E, Q94D, Q94K, Q94R, Q94N, Q94S, Q94T, Q94C, I95E, I95D, I95K, I95R, I95N, I95Q, I95S, I95T, H97E, H97D, H97K, H97R, H97N, H97Q, H97S, H97T, H97C, L98E, L98D, L98K, L98R, L98N, L98Q, L98S, L98T, L98C, V101C, V101E, V101D, V101K, V101R, V101N, V101Q, V101S, V101T, E103K, E104R, K105Q, K105D, E107R, K108Q, K108D, E109R, D110K, R113Q, R113E, K115Q, K115D, R124Q, R124D, R124E, R152Q, R152D, R165Q, and R165D in the mature IFN-β

polypeptide set forth in SEQ ID NO;

1.

54. The modified IFN-β

polypeptide of claim 49, wherein the unmodified IFN-β

polypeptide has a sequence of amino acids set forth in SEQ ID NO;

1 or SEQ ID NO;

3.

55. The modified IFN-β

polypeptide of claim 49, wherein the unmodified IFN-β

polypeptide is an allelic or species variant of the polypeptide set forth in SEQ ID NO;

1.

56. The modified IFN-β

polypeptide of claim 55, wherein the allelic or species variant has 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to the polypeptide set forth in SEQ ID NO;

1 excluding the amino acid modification(s).

57. The modified IFN-β

polypeptide of claim 49, wherein only the primary sequence is modified and the polypeptide exhibits increased conformational stability.

58. A modified IFN-β

polypeptide of claim 49, wherein;

the two or more amino acid modification(s) correspond to modifications selected from among L5E, L5D, L5K, L5R, F8E, F8D, F8K, F8R, L9E, L9D, L9K, L9R, S12E, S12D, S12K, S12R, F15E, F15D, F15K, F15R, Q16E, Q16D, Q16K, Q16R, L20E, L20D, L20K, L20R, W22E, W22D, W22K, W22R, Q23E, Q23D, Q23K, Q23R, L24E, L24D, L24K, L24R, G78E, G78D, G78K, G78R, W79E, W79D, W79K, W79R, N80E, N80D, N80K, N80R, T82E, T82D, T82K, T82R, I83E, I83D, I83K, I83R, N86E, N86D, N86K, N86R, L87E, L87D, L87K, L87R, A89E, A89D, A89K, and A89R in the mature IFN-β

polypeptide set forth in SEQ ID NO;

1; and

the amino acid modifications contribute to increased conformational stability due to the addition of charges to regions in helices A and C.

59. A modified IFN-β

polypeptide of claim 49, wherein;

the two or more amino acid modification(s) correspond to modifications selected from among M1E, M1D, M1K, M1R, M1N, M1Q, M1S, M1T, L5E, L5D, L5K, L5R, L5N, L5Q, L5S, L5T, L6E, L6D, L6K, L6R, L6N, L6Q, L6S, L6T, L9E, L9D, L9K, L9R, L9N, L9Q, L9S, L9T, Q10E, Q10D, Q10K, Q10R, Q10N, Q10S, Q10T, S13E, S13D, S13K, S13R, S13N, S13Q, S13T, N14E, N14D, N14K, N14R, N14Q, N14S, N14T, Q16E, Q16D, Q16K, Q16R, Q16N, Q16S, Q16T, C17E, C17D, C17K, C17R, C17N, C17Q, C17S, C17T, L20E, L20D, L20K, L20R, L20N, L20Q, L20S, L20T, I83E, I83D, I83K, I83R, I83N, I83Q, I83S, I83T, N86E, N86D, N86K, N86R, N86Q, N86S, N86T, L87E, L87D, L87K, L87R, L87N, L87Q, L87S, L87T, N90E, N90D, N90K, N90R, N90Q, N90S, N90T, V91E, V91D, V91K, V91R, V91N, V91Q, V91S, V91T, Q94E, Q94D, Q94K, Q94R, Q94N, Q94S, Q94T, I95E, I95D, I95K, I95R, I95N, I95Q, I95S, I95T, H97E, H97D, H97K, H97R, H97N, H97Q, H97S, H97T, L98E, L98D, L98K, L98R, L98N, L98Q, L98S, L98T, V101E, V101D, V101K, V101R, V101N, V101Q, V101S, and V101T in the mature IFN-β

polypeptide set forth in SEQ ID NO;

1; and

the amino acid modifications contribute to increased conformational stability due to increased polar interactions between helices A and C.

60. A modified IFN-β

polypeptide of claim 49, wherein;

the two or more amino acid modification(s) correspond to modifications selected from among M1C, L6C, Q10C, S13C, Q16C, N90C, V91C, Q94C, H97C, L98C, and V101C in the mature IFN-β

polypeptide set forth in SEQ ID NO;

1; and

the amino acid modifications result in introduction of a disulfide bridge in the IFN-β

polypeptide.

61. A modified IFN-β

polypeptide of claim 60, wherein the disulfide bridge formed between positions corresponds to amino acid positions C1-C101, C6-C98, C16-C90, C10-C97, C10-C98, or C13-C94 in the mature IFN-β

polypeptide set forth in SEQ ID NO;

1.

62. A modified IFN-β

polypeptide of claim 49, wherein;

the two or more amino acid modification(s) correspond to modifications selected from among E43K, E53R, D54K, E61K, E81K, E85K, E103K, E104R, E107R, E109R, and D110K in the mature IFN-β

polypeptide set forth in SEQ ID NO;

1; and

the amino acid modifications contribute to increased conformational stability due to an increase in the isoelectric point.

63. A modified IFN-β

polypeptide of claim 49, wherein;

the two or more amino acid modification(s) correspond to modifications selected from among R11D, R11Q, K45D, K45Q, K52D, K52Q, K105D, K105Q, K108D, K108Q, R113E, R113Q, K115D, K115Q, R124D, R124Q, R124E, R152D, R152Q, R165Q, and R165D in the mature IFN-β

polypeptide set forth in SEQ ID NO;

1

64. A modified IFN-β

polypeptide of claim 49, further comprising one or more amino acid modifications contributing to one or more of deimmunization, glycosylation, and PEGylation of the polypeptide.

65. A modified IFN-β

polypeptide of claim 64, wherein the polypeptide is glycosylated or conjugated to a polyethylene glycol (PEG) moiety.

96. A method of treating multiple sclerosis, comprising administering a modified IFN-β

polypeptide that exhibits increased resistance to cleavage by gelatinase B.

97. The method of claim 96, wherein the modified IFN-β

polypeptide has a sequence of amino acids set forth in any one of SEQ ID NOS;

4-11, 16, 17, 20-27, 30-36, 39-42, 45-54, 61-70, 75-87, 157, 158, 163-168, 173, 174, 180-185, 190-193, 198, 199, 204, 205, 209, 210, 213-224, 233-238, 247-250, 266-279, 282, 283, 295-310, 328-358, 377-387, 396-403, 408-411, 447-454, 474-479, 497-504, 540-542, 547, 551, 555-558, 562-576, 578-583, 585-589, 591, 604-607, 610-614, 616-650, 652, 653, 655, 656, and 658.