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US 10,647,775 B2Granted
De novo binding domain containing polypeptides and uses thereof
AssigneesSubdomain, LLC, Arcellx, Inc.
InventorsDavid William Lafleur, David M. Hilbert
Life of this patent
Estimating the term…
Abstract
Provided herein are de novo binding domain containing polypeptides (DBDpp) that specifically bind a target of interest. Nucleic acids encoding the DBDpp, and vectors and host cells containing the nucleic acids are also provided. Libraries of DBDpp, methods of producing and screening such libraries and the DBDpp identified from such libraries and screens are also encompassed. Methods of making and using the DBDpp are additionally provided. Such uses include, without limitation, affinity purification, and diagnostic and therapeutic applications.
Claims24
A method for purifying a target of interest comprising:
- (a) contacting a sample comprising a target of interest with a composition comprising:
- a polypeptide attached to a solid support, wherein the polypeptide comprises an amino acid sequence selected from the group consisting of:
- (SEQ ID NO:
- 2)
- MGSWX5X6FKX9X10LAX13IKX16X17LEALGGSEAELAX30FEX33
- X34IAX37FEX40X41LQ X44YKGKGNPEVEALRKEAAAIRDELQAY
- RHN,
- (SEQ ID NO:
- 3)
- MGSWAEFKQRLAAIKTRLEALGGSEAELAAFX32X33EIX36AFX39X40
- ELX43AYKGKGNPEVEALX57X58EAX61AIX64X65ELX68AYRHN,
- (SEQ ID NO:
- 4)
- MGSWX5EFX8X9RLX12AIX15X16RLX19ALGGSEAELAAFEKEIAAFE
- SELQAYKGKGNPEVEX55LRX58X59AAX62IRX65X66LQAYRHN,
- (SEQ ID NO:
- 5)
- MGSWX5X6FKX9X10LAX13IKX16X17LEALGGSEAELAAFX32X33EI
- X36AFX39X40ELX43AYKGKGNPEVEX55LRX58X59AAX62IRX65
- X66LQAYRHN,
- (SEQ ID NO:
- 6)
- MGSWX5EFX8X9RLX12AIX15X16RLX19ALGGSEAELAX30FEX33
- X34IAX37FEX40X41LQX44YKGKGNPEVEALX57X58EAX61AIX64
- X65ELX68AYRHN,
- (SEQ ID NO:
- 7)
- MGSWX5X6FKX9X10LAX13IKX16X17LEALZ1EAELAX28FEX31X32
- IAX35FEX38X39LQX42YZ2NPEVEALRKEAAAIRDELQAYRHN,
- (SEQ ID NO:
- 8)
- MGSWAEFKQRLAAIKTRLEALZ1EAELAAFX30X31EIX34AFX37X38E
- LX41AYZ2NPEVEALX52X53EAX56AIX59X60ELX63AYRHN,
- (SEQ ID NO:
- 9)
- MGSWX5EFX8X9RLX12AIX15X16RLX19ALZ1EAELAAFEKEIAAFES
- ELQAYZ2NPEVEX50LRX53X54AAX57IRX60X61LQAYRHN,
- (SEQ ID NO:
- 10)
- MGSWX5X6FKX9X10LAX13IKX16X17LEALZ1EAELAAFX30X31EI
- X34AFX37X38ELX41AYZ2NPEVEX50LRX53X54AAX57IRX60X61LQ
- AYRHN,
- and
- (SEQ ID NO:
- 11)
- MGSWX5EFX8X9RLX12AIX15X16RLX19ALZ1EAELAX28FEX31X32
- IAX35FEX38X39LQX42YZ2NPEVEALX52X53EAX56AIX59X60EL
- X63AYRHN,
- and combinations thereof;
- wherein Xn is a natural or non-natural amino acid, wherein each Xn is the same or different natural or non-natural amino acid,
- wherein Z1 and Z2 comprise between about 2 to about 30 natural or non-natural amino acids,
- wherein the amino acid sequence differs from SEQ ID NO:
- 1 and does not comprise SEQ ID NO:
- 50,
- wherein the polypeptide specifically binds the target of interest,
- wherein the contacting is performed under conditions that permit binding of the composition to the target of interest;
- and
- (b) removing a portion of the sample that is not bound to the composition.
55 more elements
A method for purifying a target of interest comprising,
- (a) contacting a sample comprising a target of interest with a composition comprising:
- a virus-like particle coupled to a solid support, wherein the virus-like particle expresses a polypeptide as a membrane protein, the polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:
- 7, SEQ ID NO:
- 8, SEQ ID NO:
- 9, SEQ ID NO:
- 10, and SEQ ID NO:
- 11,
- wherein no cysteine or proline residues are substituted into any of SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:
- 7, SEQ ID NO:
- 8, SEQ ID NO:
- 9, SEQ ID NO:
- 10, and SEQ ID NO:
- 11,
- wherein the amino acid sequence differs from SEQ ID NO:1 and does not comprise SEQ ID NO:
- 50,
- wherein the polypeptide specifically binds the target of interest,
- wherein the contacting is performed under conditions that permit binding of the composition to the target of interest;
- and
- (b) removing a portion of the sample that is not bound to the composition.
16 more elements
A method for removing one or more contaminants from a sample comprising a target of interest comprising,
- (a) contacting a sample comprising a target of interest with a composition comprising:
- a virus-like particle coupled to a solid support, wherein the virus-like particle expresses a polypeptide as a membrane protein, the polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:
- 7, SEQ ID NO:
- 8, SEQ ID NO:
- 9, SEQ ID NO:
- 10, and SEQ ID NO:
- 11,
- wherein no cysteine or proline residues are substituted into any of SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:
- 7, SEQ ID NO:
- 8, SEQ ID NO:
- 9, SEQ ID NO:
- 10, and SEQ ID NO:
- 11,
- wherein the amino acid sequence differs from SEQ ID NO:1 and does not comprise SEQ ID NO:
- 50,
- wherein the polypeptide specifically binds one or more contaminants to be removed from a sample comprising the target of interest,
- wherein the contacting is performed under conditions that permit binding of the composition to the one or more contaminants;
- and
- (b) collecting a portion of the sample that is not bound to the composition.
16 more elements
An affinity resin comprising a polypeptide comprising an amino acid sequence selected from the group consisting of:
- (SEQ ID NO:
- 2)
- MGSWX5X6FKX9X10LAX13IKX16X17LEALGGSEAELAX30FEX33
- X34IAX37FEX40X41LQX44YKGKGNPEVEALRKEAAAIRDELQAYR
- HN;
- (SEQ ID NO:
- 3)
- MGSWAEFKQRLAAIKTRLEALGGSEAELAAFX32X33EIX36AFX39X40
- ELX43AYKGKGNPEVEALX57X58EAX61AIX64X65ELX68AYRHN;
- (SEQ ID NO:
- 4)
- MGSWX5EFX8X9RLX12AIX15X16RLX19ALGGSEAELAAFEKEIAAFE
- SELQAYKGKGNPEVEX55LRX58X59AAX62IRX65X66LQAYRHN;
- (SEQ ID NO:
- 5)
- MGSWX5X6FKX9X10LAX13IKX16X17LEALGGSEAELAAFX32X33EI
- X36AFX39X40ELX43AYKGKGNPEVEX55LRX58X59AAX62IRX65
- X66LQAYRHN;
- (SEQ ID NO:
- 9)
- MGSWX5EFX8X9RLX12AIX15X16RLX19ALZ1EAELAAFEKEIAAFES
- ELQAYZ2NPEVEX50LRX53X54AAX57IRX60X61LQAYRHN;
- (SEQ ID NO:
- 10)
- MGSWX5X6FKX9X10LAX13IKX16X17LEALZ1EAELAAFX30X31EI
- X34AFX37X38ELX41AYZ2NPEVEX50LRX53X54AAX57IRX60X61LQ
- AYRHN;
- and
- (SEQ ID NO:
- 11)
- MGSWX5EFX8X9RLX12AIX15X16RLX19ALZ1EAELAX28FEX31X32
- IAX35FEX38X39LQX42YZ2NPEVEALX52X53EAX56AIX59X60EL
- X63AYRHN;
- and combinations thereof;
- wherein Xn is a natural or non-natural amino acid;
- wherein each Xn is the same or different natural or non-natural amino acid;
- and/or
- wherein Z1 and/or Z2 is 2 to 30 natural or non-natural amino acids;
- and wherein the amino acid sequence differs from SEQ ID NO:
- 1 and does not comprise SEQ ID NO:
- 50.
38 more elements
A method of making an affinity resin comprising a step of:
- attaching to a solid support a polypeptide comprising an amino acid sequence selected from the group consisting of:
- (SEQ ID NO:
- 2)
- MGSWX5X6FKX9X10LAX13IKX16X17LEALGGSEAELAX30FEX33
- X34IAX37FEX40X41LQX44YKGKGNPEVEALRKEAAAIRDELQAY
- RHN;
- (SEQ ID NO:
- 3)
- MGSWAEFKQRLAAIKTRLEALGGSEAELAAFX32X33EIX36AFX39X40
- ELX43AYKGKGNPEVEALX57X58EAX61AIX64X65ELX68AYRHN;
- (SEQ ID NO:
- 4)
- MGSWX5EFX8X9RLX12AIX15X16RLX19ALGGSEAELAAFEKEIAAFE
- SELQAYKGKGNPEVEX55LRX58X59AAX62IRX65X66LQAYRHN;
- (SEQ ID NO:
- 5)
- MGSWX5X6FKX9X10LAX13IKX16X17LEALGGSEAELAAFX32X33EI
- X36AFX39X40ELX43AYKGKGNPEVEX55LRX58X59AAX62IRX65
- X66LQAYRHN;
- (SEQ ID NO:
- 6)
- MGSWX5EFX8X9RLX12AIX15X16RLX19ALGGSEAELAX30FEX33
- X34IAX37FEX40X41LQX44YKGKGNPEVEALX57X58EAX61AIX64
- X65ELX68AYRHN;
- (SEQ ID NO:
- 7)
- MGSWX5X6FKX9X10LAX13IKX16X17LEALZ1EAELAX28FEX31X32
- IAX35FEX38X39LQX42YZ2NPEVEALRKEAAAIRDELQAYRHN;
- (SEQ ID NO:
- 8)
- MGSWAEFKQRLAAIKTRLEALZ1EAELAAFX30X31EIX34AFX37X38E
- LX41AYZ2NPEVEALX52X53EAX56AIX59X60ELX63AYRHN;
- (SEQ ID NO:
- 9)
- MGSWX5EFX8X9RLX12AIX15X16RLX19ALZ1EAELAAFEKEIAAFES
- ELQAYZ2NPEVEX50LRX53X54AAX57IRX60X61LQAYRHN;
- (SEQ ID NO:
- 10)
- MGSWX5X6FKX9X10LAX13IKX16X17LEALZ1EAELAAFX30X31EI
- X34AFX37X38ELX41AYZ2NPEVEX50LRX53X54AAX57IRX60X61LQ
- AYRHN;
- and
- (SEQ ID NO:
- 11)
- MGSWX5EFX8X9RLX12AIX15X16RLX19ALZ1EAELAX28FEX31X32
- IAX35FEX38X39LQX42YZ2NPEVEALX52X53EAX56AIX59X60EL
- X63AYRHN;
- and combinations thereof;
- wherein Xn is a natural or non-natural amino acid;
- wherein each Xn is the same or different natural or non-natural amino acid;
- and/or
- wherein Z1 and/or Z2 is 2 to 30 natural or non-natural amino acids;
- and wherein the amino acid sequence differs from SEQ ID NO:
- 1 and does not comprise SEQ ID NO:
- 50.
52 more elements
A composition comprising a solid support coupled to a polypeptide comprising an amino acid sequence selected from the group consisting of:
- (SEQ ID NO:
- 2)
- MGSWX5X6FKX9X10LAX13IKX16X17LEALGGSEAELAX30FEX33
- X34IAX37FEX40X41LQX44YKGKGNPEVEALRKEAAAIRDELQAY
- RHN;
- (SEQ ID NO:
- 3)
- MGSWAEFKQRLAAIKTRLEALGGSEAELAAFX32X33EIX36AFX39X40
- ELX43AYKGKGNPEVEALX57X58EAX61AIX64X65ELX68AYRHN;
- (SEQ ID NO:
- 4)
- MGSWX5EFX8X9RLX12AIX15X16RLX19ALGGSEAELAAFEKEIAAFE
- SELQAYKGKGNPEVEX55LRX58X59AAX62IRX65X66LQAYRHN;
- (SEQ ID NO:
- 5)
- MGSWX5X6FKX9X10LAX13IKX16X17LEALGGSEAELAAFX32X33EI
- X36AFX39X40ELX43AYKGKGNPEVEX55LRX58X59AAX62IRX65
- X66LQAYRHN;
- (SEQ ID NO:
- 6)
- MGSWX5EFX8X9RLX12AIX15X16RLX19ALGGSEAELAX30FEX33
- X34IAX37FEX40X41LQX44YKGKGNPEVEALX57X58EAX61AIX64
- X65ELX68AYRHN;
- (SEQ ID NO:
- 7)
- MGSWX5X6FKX9X10LAX13IKX16X17LEALZ1EAELAX28FEX31X32
- IAX35FEX38X39LQX42YZ2NPEVEALRKEAAAIRDELQAYRHN;
- (SEQ ID NO:
- 8)
- MGSWAEFKQRLAAIKTRLEALZ1EAELAAFX30X31EIX34AFX37X38E
- LX41AYZ2NPEVEALX52X53EAX56AIX59X60ELX63AYRHN;
- (SEQ ID NO:
- 9)
- MGSWX5EFX8X9RLX12AIX15X16RLX19ALZ1EAELAAFEKEIAAFES
- ELQAYZ2NPEVEX50LRX53X54AAX57IRX60X61LQAYRHN;
- (SEQ ID NO:
- 10)
- MGSWX5X6FKX9X10LAX13IKX16X17LEALZ1EAELAAFX30X31EI
- X34AFX37X38ELX41AYZ2NPEVEX50LRX53X54AAX57IRX60X61LQ
- AYRHN;
- and
- (SEQ ID NO:
- 11)
- MGSWX5EFX8X9RLX12AIX15X16RLX19ALZ1EAELAX28FEX31X32
- IAX35FEX38X39LQX42YZ2NPEVEALX52X53EAX56AIX59X60EL
- X63AYRHN;
- and
- combinations thereof;
- wherein Xn is a natural or non-natural amino acid;
- wherein each Xn is the same or different natural or non-natural amino acid;
- and/or
- wherein Z1 and/or Z2 is 2 to 30 natural or non-natural amino acids;
- and
- wherein the amino acid sequence differs from SEQ ID NO:
- 1 and does not comprise SEQ ID NO:
- 50.
53 more elements
A composition comprising a polypeptide conjugated to a detectable agent and/or tag,
- wherein the polypeptide comprises an amino acid sequence selected from the group consisting of:
- (SEQ ID NO:
- 2)
- MGSWX5X6FKX9X10LAX13IKX16X17LEALGGSEAELAX30FEX33
- X34IAX37FEX40X41LQX44YKGKGNPEVEALRKEAAAIRDELQAY
- RHN;
- (SEQ ID NO:
- 3)
- MGSWAEFKQRLAAIKTRLEALGGSEAELAAFX32X33EIX36AFX39X40
- ELX43AYKGKGNPEVEALX57X58EAX61AIX64X65ELX68AYRHN;
- (SEQ ID NO:
- 4)
- MGSWX5EFX8X9RLX12AIX15X16RLX19ALGGSEAELAAFEKEIAAFE
- SELQAYKGKGNPEVEX55LRX58X59AAX62IRX65X66LQAYRHN;
- (SEQ ID NO:
- 5)
- MGSWX5X6FKX9X10LAX13IKX16X17LEALGGSEAELAAFX32X33EI
- X36AFX39X40ELX43AYKGKGNPEVEX55LRX58X59AAX62IRX65
- X66LQAYRHN;
- (SEQ ID NO:
- 6)
- MGSWX5EFX8X9RLX12AIX15X16RLX19ALGGSEAELAX30FEX33
- X34IAX37FEX40X41LQX44YKGKGNPEVEALX57X58EAX61AIX64
- X65ELX68AYRHN;
- (SEQ ID NO:
- 7)
- MGSWX5X6FKX9X10LAX13IKX16X17LEALZ1EAELAX28FEX31X32
- IAX35FEX38X39LQX42YZ2NPEVEALRKEAAAIRDELQAYRHN;
- (SEQ ID NO:
- 8)
- MGSWAEFKQRLAAIKTRLEALZ1EAELAAFX30X31EIX34AFX37X38E
- LX41AYZ2NPEVEALX52X53EAX56AIX59X60ELX63AYRHN;
- (SEQ ID NO:
- 9)
- MGSWX5EFX8X9RLX12AIX15X16RLX19ALZ1EAELAAFEKEIAAFES
- ELQAYZ2NPEVEX50LRX53X54AAX57IRX60X61LQAYRHN;
- (SEQ ID NO:
- 10)
- MGSWX5X6FKX9X10LAX13IKX16X17LEALZ1EAELAAFX30X31EI
- X34AFX37X38ELX41AYZ2NPEVEX50LRX53X54AAX57IRX60X61LQ
- AYRHN;
- and
- (SEQ ID NO:
- 11)
- MGSWX5EFX8X9RLX12AIX15X16RLX19ALZ1EAELAX28FEX31X32
- IAX35FEX38X39LQX42YZ2NPEVEALX52X53EAX56AIX59X60EL
- X63AYRHN;
- and
- combinations thereof;
- wherein Xn is a natural or non-natural amino acid;
- wherein each Xn is the same or different natural or non-natural amino acid;
- and/or
- wherein Z1 and/or Z2 is 2 to 30 natural or non-natural amino acids;
- and
- wherein the amino acid sequence differs from SEQ ID NO:
- 1 and does not comprise SEQ ID NO:
- 50.
54 more elements
Dependencies are inferred from the claim text.