Systems and methods for identifying mutants

A computer readable storage medium storing one or more programs, the one or more programs comprising instructions, which when executed by an electronic device with one or more processors and a memory cause the electronic device to identify one or more combinatorial substitutions that affect a first property of a target protein by a method comprising:

• A) obtaining an identity of each single point mutation in a first plurality of single point mutations of the target protein, each respective single point mutation in the first plurality of single point mutations defining a corresponding single point substituted protein characterized by a reference sequence for the target protein with the exception of an alteration at a respective independent position within the reference sequence to an amino acid other than that found in the reference sequence;
• B) obtaining, for each corresponding point substituted protein defined by the first plurality of single point mutations, a corresponding set of values for a set of properties of the corresponding point substituted protein, wherein the set of properties comprises:
• (i) a stability of the corresponding point substituted protein,
• (ii) at least one protein formulation property of the corresponding point substituted protein, and
• (iii) a determination that the respective single point mutation in the corresponding point substituted protein occurs at a predetermined position that exhibits variability across a plurality of naturally occurring homologs of the target protein;
• C) filtering the first plurality of single point mutations to form a second plurality of single point mutations based at least upon each corresponding set of values for the set of properties, wherein the filtering includes determining,
• for each corresponding point substituted protein defined by the first plurality of single point mutations,
• for each respective property in the set of properties,
• whether a value of the respective property in the corresponding set of values for the corresponding point substituted protein satisfies a corresponding threshold value requirement for the respective property, wherein
• the corresponding point substituted protein is included in the second plurality of single point mutations when each corresponding threshold value requirement for each property in the set of properties is satisfied, and
• the corresponding point substituted protein is not included in the second plurality of single point mutations when any corresponding threshold value requirement of any property in the set of properties is not satisfied;
• D) obtaining a corresponding measured value of the first property for each combinatorially substituted protein in a first plurality of combinatorially substituted proteins, wherein each respective combinatorially substituted protein in the first plurality of combinatorially substituted proteins is characterized by the reference sequence for the target protein with the exception of the independent inclusion of two or more single point mutations from the second plurality of single point mutations;
• E) training a surrogate model within an N-dimensional space, wherein N is a positive integer of 10 or greater, using at least, for each respective combinatorially substituted protein in the first plurality of combinatorially substituted proteins, the corresponding measured value of the first property in the respective combinatorially substituted proteins against an identity of each single point mutation in the respective combinatorially substituted protein, wherein the model comprises 20 or more parameters and the first plurality of combinatorially substituted proteins comprises 20 or more proteins;
• F) using the surrogate model and, for each respective combinatorially substituted protein in the first plurality of combinatorially substituted proteins, the identity of each single point mutation in the respective combinatorially substituted protein, to update a search model;
• and
• G) using the updated search model to identify a second plurality of combinatorially substituted proteins within the N-dimensional space, wherein each respective combinatorially substituted protein in the second plurality of combinatorially substituted proteins is characterized by the reference sequence for the target protein with the exception of independent inclusion of two or more single point mutations from the second plurality of single point mutations.

A method comprising:

• A) obtaining an identity of each single point mutation in a first plurality of single point mutations of the target protein, each respective single point mutation in the first plurality of single point mutations defining a corresponding single point substituted protein characterized by a reference sequence for the target protein with the exception of an alteration at a respective independent position within the reference sequence to an amino acid other than that found in the reference sequence;
• B) obtaining, for each corresponding point substituted protein defined by the first plurality of single point mutations, a corresponding set of values for a set of properties of the corresponding point substituted protein, wherein the set of properties comprises:
• (i) a stability of the corresponding point substituted protein,
• (ii) at least one protein formulation property of the corresponding point substituted protein, and
• (iii) a determination that the respective single point mutation in the corresponding point substituted protein occurs at a predetermined position that exhibits variability across a plurality of naturally occurring homologs of the target protein;
• C) filtering the first plurality of single point mutations to form a second plurality of single point mutations based at least upon each corresponding set of values for the set of properties, wherein the filtering includes determining,
• for each corresponding point substituted protein defined by the first plurality of single point mutations,
• for each respective property in the set of properties,
• whether a value of the respective property in the corresponding set of values for the corresponding point substituted protein satisfies a corresponding threshold value requirement for the respective property, wherein
• the corresponding point substituted protein is included in the second plurality of single point mutations when each corresponding threshold value requirement for each property in the set of properties is satisfied, and
• the corresponding point substituted protein is not included in the second plurality of single point mutations when any corresponding threshold value requirement of any property in the set of properties is not satisfied;
• D) obtaining a corresponding measured value of the first property for each combinatorially substituted protein in a first plurality of combinatorially substituted proteins, wherein each respective combinatorially substituted protein in the first plurality of combinatorially substituted proteins is characterized by the reference sequence for the target protein with the exception of the independent inclusion of two or more single point mutations from the second plurality of single point mutations;
• E) training a surrogate model within an N-dimensional space, wherein N is a positive integer of 10 or greater, using at least, for each respective combinatorially substituted protein in the first plurality of combinatorially substituted proteins, the corresponding measured value of the first property in the respective combinatorially substituted proteins against an identity of each single point mutation in the respective combinatorially substituted protein, wherein the model comprises 20 or more parameters and the first plurality of combinatorially substituted proteins comprises 20 or more proteins;
• F) using the surrogate model and, for each respective combinatorially substituted protein in the first plurality of combinatorially substituted proteins, the identity of each single point mutation in the respective combinatorially substituted protein, to update a search model;
• and
• G) using the updated search model to identify a second plurality of combinatorially substituted proteins within the N-dimensional space, wherein each respective combinatorially substituted protein in the second plurality of combinatorially substituted proteins is characterized by the reference sequence for the target protein with the exception of independent inclusion of two or more single point mutations from the second plurality of single point mutations.