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1. WO2019165148 - DETERMINING CONDITIONS FOR PURIFICATION OF PROTEINS

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[ EN ]

CLAIMS

WHAT IS CLAIMED IS:

1. A method comprising:

providing a plate having a plurality of wells, wherein individual wells of the plurality of wells include (i) a stationary phase material of a column chromatography system, (ii) an amount of a protein, and (iii) an amount of a solution having a pH and a concentration of a salt; wherein each well of the plurality of wells has a different combination of the stationary phase material, pH, and concentration of the salt;

determining a measure of performance for each well of the plurality of wells, the measure of performance of an individual well of the plurality of wells indicating adsorption of the protein with respect to the stationary phase material included in the individual well;

generating, based at least partly on the measures of performance for each well of the plurality of wells, a plurality of models to predict, based at least partly on a set of conditions for a chromatography column, a yield and a purity of the protein for a plurality of stationary phase materials, wherein:

each model of the plurality of models is associated with an individual stationary phase material of the plurality of stationary phase materials;

each model of the plurality of models is associated with a different stationary phase material of the plurality of stationary phase materials; and the set of conditions includes a range of pH values and a range of salt concentrations;

generating, using the plurality of models, purification conditions including at least one pH value of the range of pH values, at least one salt concentration of the range of salt concentrations, and one or more stationary phase materials of the plurality of stationary phase materials that maximize a combination of the yield and the purity of the protein and minimize a cost of performing a chromatographic process at the at least one pH value and the at least one salt concentration with respect to the one or more stationary phase materials.

2. The method of claim 1, wherein the one or more stationary phase materials are determined based at least partly on a durability of individual stationary phase materials of the plurality of stationary phase materials, an amount of the individual stationary phase materials to be utilized in a chromatography column to purify the protein, a size of the chromatography column, or combinations thereof.

3. The method of claim 1 or 2, wherein the purification conditions indicate that the protein is to be purified utilizing a first stationary phase material at a first pH value and a first salt concentration followed by purification of the protein utilizing a second stationary phase material different from the first stationary phase material at a second pH value different from the first pH value and a second salt concentration different from the first salt concentration.

4. The method of any one of claims 1-3, wherein the measures of performance include a yield, a purity, a characteristic of the solution after a period of time, a property of a remaining amount of the protein included in the solution after the period of time, or combinations thereof.

5. A method comprising:

generating yield data and purity data for a number of proteins, the yield data and the purity data indicating yield and purity for each of a plurality of proteins over a range of pH values, over a range of salt concentrations, and for a stationary phase material of a column chromatography technique;

obtaining sequence data indicating at least a portion of amino acid sequences of individual proteins of the plurality of proteins;

obtaining structure data indicating one or more structures exhibited by individual proteins of the plurality of proteins;

generating characterization data for the plurality of proteins, the characterization data including values obtained from analytical tests that indicate values of properties of the plurality of proteins;

generating a model to predict, at one or more pH values and one or more salt concentration values, yield and purity of an additional protein for the stationary phase material, wherein the model includes a sequence component that indicates a similarity between the amino acid sequences of the plurality of proteins and an additional amino acid sequence of the additional protein and a characterization component that indicates similarities between values of the properties for the plurality of proteins and additional values of the properties for the additional protein.

6. The method of claim 5, wherein the yield data and the purity data are determined from running a number of chromatography columns for a number of different proteins using the stationary phase material over the range of pH values and the range of salt concentrations.

7. The method of claim 5 or 6, wherein the yield data and the purity data are determined by analyzing solutions obtained from wells of a multi-well plate, individual wells of the multi-well plate including an amount of a solution including the protein and having a pH level and a salt concentration and including an amount of the stationary phase material.

8. The method of any one of claims 5-7, wherein the one or more structures includes hydrophobic regions, polar regions, folds, turns, loops, or combinations thereof.

9. The method of any one of claims 5-8, wherein:

the additional protein and the number of proteins each include a common secondary structure;

at least a portion of an amino acid sequence of the additional protein and at least a portion of the amino acid sequences of the number of proteins have at least 75% identity; and

the analytical tests produce values of one or more biophysical properties of the number of proteins and a range of values for a biophysical property of the one or more biophysical properties for the additional protein is within at least about 90% of a range of values for the biophysical property for the number of proteins.

10. The method of any one of claims 5-9, wherein the characterization data is related to at least one of differential scanning fluorimetry measurements for the number of proteins, molecular weight of the number of proteins, turbidity of solutions including the number of proteins, or combinations thereof.

11. A method comprising:

providing a plate having a plurality of wells, wherein individual wells of the plurality of wells include (i) a stationary phase material of a column chromatography system, (ii) an amount of a protein, and (iii) an amount of a solution having a pH and a concentration of a salt; wherein:

each well of the plurality of wells has a different combination of the stationary phase material, pH, and concentration of the salt;

the pH associated with each well of the plurality of wells is included in a range of pH values;

the concentration of the salt associated with each well of the plurality of wells is included in a range of salt concentration values; and

a first individual stationary phase material of a first number of wells of the plurality of wells is different from a second individual stationary phase material of a second number of wells of the plurality of wells;

determining a measure of performance for each well of the plurality of wells, the measure of performance of an individual well of the plurality of wells indicating adsorption of the protein with respect to the stationary phase material included in the individual well;

generating, based at least partly on individual measures of performance for the first number of wells, a first model to predict an additional measure of performance for an additional protein with respect to the first individual stationary phase material, the range of pH values, and the range of salt concentration values;

generating, based at least partly on a subset of the individual measures of performance for the first number of wells, a second model to predict the additional measure of performance for the additional protein with respect to the first individual stationary phase material, the range of pH values, and the range of salt concentration values;

performing a comparison between first results for the additional measure of performance generated from the first model and second results for the additional measure of performance generated from the second model; and

determining, based at least partly on the comparison, a metric indicating a similarity between the first results and the second results.

12. The method of claim 11, wherein the metric indicates an amount of error between the first results and the second results.

13. The method of claim 11 or 12, wherein the first measure of performance includes a first combination of yield and purity values and the second measure of performance includes a second combination of yield and purity values.

14. The method of any one of claims 11-13, wherein the range of pH values is from about 3 to 8.5 and the range of salt concentrations is from about 30 millimolar (mM) to about 700 mM.

15. The method of any one of claims 11-14, wherein the stationary phase material is related to ion exchange chromatography, high pressure liquid chromatography, mixed mode chromatography, hydrophobic interaction chromatography, size exclusion chromatography, affinity chromatography, hydroxyapatite, reversed phase chromatography, or combinations thereof.

16. The method of any one of claims 11-15, wherein the second model is derived by iteratively selecting a subset of the plurality of wells and determining an amount of error between measures of performance of the subset of wells and the measure of performance for each well of the plurality of wells until the amount of error is minimized.

17. A method comprising:

providing a plate having a plurality of wells, wherein individual wells of the plurality of wells include (i) a stationary phase material of a plurality of stationary phase materials for column chromatography systems, (ii) an amount of a protein, and (iii) an amount of a solution having a pH and a concentration of a salt; wherein each well of the plurality of wells has a different combination of the stationary phase material, pH, and concentration of the salt;

determining a measure of performance for each well of the plurality of wells, the measure of performance of an individual well of the plurality of wells indicating adsorption of the protein with respect to the stationary phase material included in the individual well;

determining, based at least partly on individual measures of performance for the plurality of wells, chromatography conditions for a subset of the wells, the chromatography conditions including a pH value and a salt concentration for each well of the subset of wells;

generating a plurality of models for the plurality of stationary phase materials to predict yield and purity of one or more chromatography processes based at least partly on at least one of amino acid sequences of proteins, one or more structures of the proteins, or characterization data for the proteins, the characterization data including values obtained from analytical instruments that indicate properties of the proteins; generating, based at least partly on the chromatography conditions and the plurality of models, at least one pH value of the range of pH values, at least one salt concentration of the range of salt concentrations, and one or more stationary phase materials of the plurality of stationary phase materials to maximize yield and purity of the protein.

18. The method of claim 17, further comprising:

predicting, based at least partly on at least one model of the plurality of models, a predicted yield value and a predicted purity value for a combination of a particular pH value, a particular salt concentration value, and at least one particular chromatographic technique; and

aggregating predicted yield values and predicted purity values for a plurality of combinations of pH values, salt concentration values, and chromatographic techniques to produce an aggregated data set.

19. The method of claim 18, further comprising:

generating a user interface including the aggregated data set, the user interface including a plurality of selectable options, individual selectable options corresponding to a respective combination of pH value, salt concentration value, and at least one chromatographic technique.

20. The method of claim 19, further comprising:

receiving data indicating selection of a particular selectable option of the plurality of selectable option; and

in response to receiving the data, causing the user interface to display at least the chromatography technique, the pH values, the salt concentration value, and an indicator of monetary cost corresponding to the selectable option.