Hemagglutinin Polypeptides, and Reagents and Methods Relating Thereto

• US 20100061990A1
• Filed: 08/14/2007
• Published: 03/11/2010
• Est. Priority Date: 08/14/2006
• Status: Abandoned Application

• Current Assignee: Massachusetts Institute of Technology
• Original Assignee: Massachusetts Institute of Technology
• Inventors: Sasisekharan, Viswanathan, Chandrasekaran, Aarthi, Sasisekharan, Ram, Viswanathan, Karthik, Raman, Rahul, Srinivasan, Aravind, Raguram, S.
• Application Number:
  US12/301,126
• Publication Number:
  US 20100061990A1
• Time in Patent Office: Days
• US Class Current: 424/139.100
• CPC Class Codes: A61P 31/16 for influenza or rhinoviruses
• CPC Class Codes: A61P 37/04 Immunostimulants
• CPC Class Codes: G01N 2400/10 Polysaccharides, i.e. having more than five saccharide radicals attached to each other by glycosidic linkages; Derivatives thereof, e.g. ethers, esters
• CPC Class Codes: G01N 33/5308 for analytes not provided for elsewhere, e.g. nucleic acids, uric acid, worms, mites

Abstract

The present invention provides a system for analyzing interactions between glycans and interaction partners that bind to them. The present invention also provides HA polypeptides that bind to umbrella-topology glycans, and reagents and methods relating thereto.

Claims

1-35. -35. (canceled)

36. A pharmaceutical composition comprising:

an agent that competes a glycan-HA polypeptide interaction between umbrella-topology glycans and an HA polypeptide.

37. The pharmaceutical composition of claim 36, wherein the HA polypeptide is on the surface of a virus particle.

38. The pharmaceutical composition of claim 36, wherein residues of the HA polypeptide involved in the interaction include those selected from the group consisting of residues 137, 145, 156, 159, 186, 187, 189, 190, 192, 193, 196, 222, 225, 226, and 228, and combinations thereof.

39. The pharmaceutical composition of claim 36, wherein the umbrella topology glycans comprise long α

2-6 sialylated glycans.

40. The pharmaceutical composition of claim 39, wherein the long α

2-6 sialylated glycans are selected from the group consisting of Neu5Acα

2-6Galβ

1-4GlcNAcβ

1-3Galβ

1-4GlcNAc, Neu5Acα

2-6GalNAcβ

1-4GlcNAcβ

1-3GalNAcβ

1-4GlcNAc, Neu5Acα

2-6Galβ

1-4GlcNAcβ

1-3Galβ

1-4GalNAc, Neu5Acα

2-6Galβ

1-4GlcNAcβ

1-3Galβ

1-4GlcNAcβ

1-3Galβ

1-3GalNAc, Neu5Acα

2-6GalNAcβ

1-4GlcNAcβ

1-3Galβ

1-4GalNAc, Neu5Acα

2-6GalNAcβ

1-4GlcNAcβ

1-3GalNAcβ

1-4GlcNAcβ

1-3Galβ

1-3GalNAc, NeuAcα

2-3Galβ

1-3GalNAcα

2-6Neu5Ac, Neu5Acα

2-6Galβ

1-4GlcNAcβ

1-3/6GalNAc, Neu5Acα

2-6Galβ

1-4GlcNAcβ

1-3Galβ

1-4GlcNAcβ

1-3/6GalNAc, Neu5Acα

2-6GalNAcβ

1-4GlcNAcβ

1-3/6GalNAc, Neu5Acα

2-6GalNAcβ

1-4GlcNAcβ

1-3GalNAcβ

1-4GlcNAcβ

1-3/6GalNAc, NeuAcα

2-6Galβ

1-4GalNAcβ

1-6GlcNAcβ

1-3Galα

2-3Neu5Ac, NeuAcα

2-6Galβ

1-4GalNAcβ

1-3/6GlcNAcβ

1-3/6Galα

2-3/6Neu5Ac, Neu5Acα

2-6Galβ

1-3GalNAcβ

1-4Galα

1-3Galβ

1-4Glc, Neu5Acα

2-6Galβ

1-3GalNAcβ

1-3Galα

1-4Galβ

1-4Glc, Neu5Acα

2-6Galβ

1-3GlcNAcβ

1-3Galβ

1-4Glc and Neu5Acα

2-6Galβ

1-4GlcNAcβ

1-3Galβ

1-4Glc.

41. The pharmaceutical composition of claim 36, wherein the agent is selected from the group consisting of:

glycans, small molecules, and glycomimetics.

42. The pharmaceutical composition of claim 36, wherein the agent is a polypeptide.

43. The pharmaceutical composition of claim 42, wherein the agent is an HA polypeptide.

44. The pharmaceutical composition of claim 42, wherein the agent is an HA polypeptide variant.

45. The pharmaceutical composition of claim 36, wherein the agent binds to umbrella topology glycans with an affinity that is at least 25%, at least 50%, or at least 75% of that observed under comparable conditions for a wild type HA that mediates infection of humans.

46. The pharmaceutical composition of claim 36, wherein the agent binds to umbrella topology glycans more strongly than it binds to cone topology glycans.

47. The pharmaceutical composition of claim 46, wherein the agent shows a relative affinity for umbrella topology glycans vs cone topology glycans of at least 10, at least 9, at least 8, at least 7, at least 6, at least 5, at least 4, at least 3 or at least 2.

48. The pharmaceutical composition of claim 36, wherein the interaction occurs between the HA polypeptide and receptors found on human upper respiratory epithelial cells, the bronchus and/or trachea, and/or the deep lung.

49. A method of identifying agents that compete with a glycan-HA polypeptide interaction by:

providing a collection of test agents;

contacting the test agents with at least one umbrella-topology glycan and at least one HA polypeptide that binds to the umbrella-topology glycan; and

determining that observed binding between the at least one umbrella-topology glycan and the at least one HA polypeptide is reduced when the agent is present as compared with when it is absent.

51. The method of claim 49, wherein residues of the HA polypeptide involved in the interaction include those selected from the group consisting of residues 137, 145, 156, 159, 186, 187, 189, 190, 192, 193, 196, 222, 225, 226, and 228, and combinations thereof.

52. The method of claim 49 or 50, wherein the umbrella topology glycans comprise long α

2-6 sialylated glycans.

53. The method of claim 52, wherein the long α

2-6 sialylated glycans are selected from the group consisting of Neu5Acα

2-6Galβ

1-4GlcNAcβ

1-3Galβ

1-4GlcNAc, Neu5Acα

2-6GalNAcβ

1-4GlcNAcβ

1-3GalNAcβ

1-4GlcNAc, Neu5Acα

2-6Galβ

1-4GlcNAcβ

1-3Galβ

1-4GalNAc, Neu5Acα

2-6Galβ

1-4GlcNAcβ

1-3Galβ

1-4GlcNAcβ

1-3Galβ

1-3GalNAc, Neu5Acα

2-6GalNAcβ

1-4GlcNAcβ

1-3Galβ

1-4GalNAc, Neu5Acα

2-6GalNAcβ

1-4GlcNAcβ

1-3GalNAcβ

1-4GlcNAcβ

1-3Galβ

1-3GalNAc, NeuAcα

2-3Galβ

1-3GalNAcα

2-6Neu5Ac, Neu5Acα

2-6Galβ

1-4GlcNAcβ

1-3/6GalNAc, Neu5Acα

2-6Galβ

1-4GlcNAcβ

1-3Galβ

1-4GlcNAcβ

1-3/6GalNAc, Neu5Acα

2-6GalNAcβ

1-4GlcNAcβ

1-3/6GalNAc, Neu5Acα

2-6GalNAcβ

1-4GlcNAcβ

1-3GalNAcβ

1-4GlcNAcβ

1-3/6GalNAc, NeuAcα

2-6Galβ

1-4GalNAcβ

1-6GlcNAcβ

1-3Galα

2-3Neu5Ac, NeuAcα

2-6Galβ

1-4GalNAcβ

1-3/6GlcNAcβ

1-3/6Galα

2-3/6Neu5Ac, Neu5Acα

2-6Galβ

1-3GalNAcβ

1-4Galα

1-3Galβ

1-4Glc, Neu5Acα

2-6Galβ

1-3GalNAcβ

1-3Galα

1-4Galβ

1-4Glc, Neu5Acα

2-6Galβ

1-3GlcNAcβ

1-3Galβ

1-4Glc and Neu5Acα

2-6Galβ

1-4GlcNAcβ

1-3Galβ

1-4Glc.

54. The method of claim 49 or 50, wherein the test agent is selected from the group consisting of:

glycans, small molecules, and glycomimetics.

55. The method of claim 49 or 50, wherein the test agent is a polypeptide.

56. The method of claim 49 or 50, wherein the test agent is an HA polypeptide.

57. The method of claim 49 or 50, wherein the test agent is an HA polypeptide variant.

58. The method of claim 49 or 50, wherein the test agent binds to umbrella topology glycans with an affinity that is at least 25%, at least 50%, or at least 75% of that observed under comparable conditions for a wild type HA that mediates infection of humans.

59. The method of claim 49 or 50, wherein the test agent binds to umbrella topology glycans more strongly than it binds to cone topology glycans.

60. The method of claim 49 or 50, wherein the test agent shows a relative affinity for umbrella topology glycans vs cone topology glycans of at least 10, at least 9, at least 8, at least 7, at least 6, at least 5, at least 4, at least 3 or at least 2.

50. A method of identifying agents with high affinity for umbrella-topology glycans by:

providing a collection of test agents;

contacting the test agents with at least one umbrella-topology glycan; and

determining that observed binding between the at least one umbrella-topology glycan and the test agent occurs with high affinity.

61. A method of detecting HA polypeptides in a sample, wherein the HA polypeptides bind to umbrella topology glycans.

62. The method of claim 61, wherein the sample is a pathological sample.

63. The method of claim 62, wherein the pathological sample is selected from the group consisting of blood, serum/plasma, peripheral blood mononuclear cells/peripheral blood lymphocytes (PBMC/PBL), sputum, urine, feces, throat swabs, dermal lesion swabs, cerebrospinal fluids, cervical smears, pus samples, food matrices, tissues from brain, spleen, and liver, and combinations thereof.

64. The method of claim 61, wherein the sample is an environmental sample.

65. The method of claim 64, wherein the environmental sample is selected from the group consisting of soil, water, and flora.

66. The method of claim 61, wherein the sample is a laboratory sample.

67. The method of claim 66, wherein the laboratory sample comprises engineered HA polypeptides designed and/or prepared by researchers.

68. The method of claim 61, wherein the umbrella topology glycans comprise long α

2-6 sialylated glycans.

69. A method of evaluating a test agent with high affinity for umbrella-topology glycans comprising,

determining the ability of the agent to bind to an HA having an umbrella topology glycan,

thereby evaluating the agent.

70. A device containing an agent with high affinity for umbrella-topology glycans and configured to administer a dose of an agent to the respiratory tract of a subject.

71. A glycan array comprising glycan structures of at least about 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90% 95%, or more of glycans found on HA receptors in human upper respiratory tract tissues.

72. An antibody that binds to an umbrella-topology glycan.