Crystal structures of heterodimeric Fc domains

Patent metadata

Field	Value
Publication number	US-9988460-B2
Application number	US-201715675248-A
Country	US
Kind code	B2
Filing date	Aug 11, 2017
Priority date	Nov 4, 2011
Publication date	Jun 5, 2018
Grant date	Jun 5, 2018

Abstract

Disclosed are the atomic coordinates of compositions comprising Fc heterodimer proteins in crystalline form derived from high resolution x-ray diffraction. Further disclosed are systems and methods for using all or a portion of these atomic coordinates to identify and design improved Fc heterodimer proteins. Further disclosed are compositions comprising a mixture of (i) a solubilized Fc heterodimer protein and (ii) a mother liquor solution. The mother liquor solution comprises between 2% and 10% (v/v) ethylene glycol, between 10% and 25% (w/v) polyethylene glycol having an average molecular weight of between 2000 Daltons and 10000 Daltons, and between 0.05 M and 0.40 M ammonium iodide. Further disclosed are systems and methods of identifying a mutation which promotes heterodimeric Fc chain pair formation in which structure based modeling is performed to identify a candidate mutation to an Fc chain using all or a portion of the disclosed three-dimensional atomic coordinates.

First claim

We claim:

1. A method of identifying a mutation which promotes heterodimeric Fc chain pair formation, the method comprising:
performing structure based modeling, using a suitably programmed computer, to identify a candidate mutation to an Fc chain using a three-dimensional atomic crystal structure of an Fc heterodimer protein which is defined by the atomic coordinates of any combination of chains a, b, A, and B of FIG. 26 or 27 determined from an X-ray diffraction quality crystal of the Fc heterodimer protein, wherein the Fc heterodimer protein comprises the amino acid sequences as set forth in (i) SEQ ID NOS: 2 and 3 or (ii) SEQ ID NOS: 4 and 5, and the X-ray diffraction quality crystal is in an orthorhombic space group.

2. The method of claim 1 , wherein the orthorhombic space group is P2 1 2 1 2 1 and has unit cell dimensions a=49±2 Å, b=75±2 Å, c=149±2 Å, α=β=γ=90°.

3. The method of claim 1 , wherein the structure based modeling comprises:
(a) identifying a plurality of residues on the three-dimensional atomic crystal structure that influence heterodimeric Fc chain pair formation;
(b) modeling a plurality of three-dimensional Fc structures using the three-dimensional atomic crystal structure as a template, wherein each three-dimensional Fc structure in the plurality of three-dimensional Fc structures includes mutations to one or more of the residues in the plurality of residues;
(c) comparing each three-dimensional Fc structure in the plurality of three-dimensional Fc structures to the three-dimensional atomic crystal structure; and
(d) selecting one of the three-dimensional Fc structures in the plurality of three-dimensional Fc structures based on the comparing (c).

4. The method of claim 3 , wherein the comparing (c) compares a calculated thermodynamic property of the three-dimensional atomic crystal structure to a calculated thermodynamic property of a three-dimensional Fc structure in the plurality of three-dimensional Fc structures.

5. The method of claim 4 , wherein the thermodynamic property is entropy, average energy, average enthalpy, free energy or heat capacity.

6. The method of claim 3 , wherein the comparing (c) compares a physical property of the three-dimensional atomic crystal structure to a calculated thermodynamic property of a three-dimensional Fc structure in the plurality of three-dimensional Fc structures, wherein the physical property is selected from the group consisting of (i) one or more electrostatic interactions, (ii) one or more polar interactions, (iii) one or more hydrogen-bond interactions, (iv) a comparison of buried versus accessible surface area, (v) accessible surface area, (vi) one or more hydrophobic interactions, and (vii) presence or absence of one or more buried water molecules.

7. The method of claim 3 further comprising:
(e) expressing an Fc protein having an amino acid sequence of the selected three-dimensional Fc structure in a host cell, and
(f) evaluating one or more properties of the Fc protein in vitro.

8. The method of claim 7 , wherein the one or more properties are stability, Fc effector function, a pharmacokinetic property, or a combination thereof.

9. A method of identifying a mutation which promotes heterodimeric Fc chain pair formation, the method comprising:
performing structure based modeling, using a suitably programmed computer, to identify a candidate mutation to an Fc chain using a three-dimensional atomic crystal structure defined by atomic coordinates derived from an X-ray diffraction quality crystal of an Fc heterodimer protein, the X-ray diffraction quality crystal being of space group is P2 1 2 1 2 1 and having unit cell dimensions a=49±2 Å, b=75±2 Å, c=149±2 Å, α=β=γ=90°, and the Fc heterodimer protein comprising the amino acid sequences as set forth in (i) SEQ ID NOS: 2 and 3, or (ii) SEQ ID NOS: 4 and 5.

10. The method of claim 9 , wherein the structure based modeling comprises:
(a) identifying a plurality of residues on the three-dimensional atomic crystal structure that influence heterodimeric Fc chain pair formation;
(b) modeling a plurality of three-dimensional Fc structures using the three-dimensional atomic crystal structure as a template, wherein each three-dimensional Fc structure in the plurality of three-dimensional Fc structures includes mutations to one or more of the residues in the plurality of residues;
(c) comparing each three-dimensional Fc structure in the plurality of three-dimensional Fc structures to the three-dimensional atomic crystal structure; and
(d) selecting one of the three-dimensional Fc structures in the plurality of three-dimensional Fc structures based on the comparing (c).

11. The method of claim 10 , wherein the comparing (c) compares a calculated thermodynamic property of the three-dimensional atomic crystal structure to a calculated thermodynamic property of a three-dimensional Fc structure in the plurality of three-dimensional Fc structures.

12. The method of claim 11 , wherein the thermodynamic property is entropy, average energy, average enthalpy, free energy or heat capacity.

13. The method of claim 10 , wherein the comparing (c) compares a physical property of the three-dimensional atomic crystal structure to a calculated thermodynamic property of a three-dimensional Fc structure in the plurality of three-dimensional Fc structures, wherein the physical property is selected from the group consisting of (i) one or more electrostatic interactions, (ii) one or more polar interactions, (iii) one or more hydrogen-bond interactions, (iv) a comparison of buried versus accessible surface area, (v) accessible surface area, (vi) one or more hydrophobic interactions, and (vii) presence or absence of one or more buried water molecules.

14. The method of claim 10 further comprising:
(e) expressing an Fc protein having an amino acid sequence of the selected three-dimensional Fc structure in a host cell, and
(f) evaluating one or more properties of the Fc protein in vitro.

15. The method of claim 14 , wherein the one or more properties are stability, Fc effector function, a pharmacokinetic property, or a combination thereof.

Assignees

• Zymeworks Inc

Inventors

• Spreter Von Kreudenstein Thomas
• Dixit Surjit Bhimarao
• Lario Paula Irene
• Escobar-Cabrera Eric
• Boulanger Martin J
• Suits Michael D L

Classifications

• A61P35/00

  Antineoplastic agents · CPC title

• A61P37/02

  Immunomodulators · CPC title

• C07K16/468

  Immunoglobulins having two or more different antigen binding sites, e.g. multifunctional antibodies · CPC title

• C07K16/2887

  against CD20 · CPC title

• C07K2317/526

  CH3 domain · CPC title