Method for protein kinase activity ranking
Inventors
Cutillas, Pedro Rodriguez • Wilkes, Edmund • CASADO-IZQUIERDO, Pedro
Assignees
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Publication Number
US-12360118-B2
Publication Date
2025-07-15
Expiration Date
Abstract
The present invention provides a method of quantifying the activity of a protein modifying enzyme in a sample, comprising calculating the value K for said protein-modifying enzyme on the basis of the number of modified peptides in a sample that are substrates of said protein modifying enzyme, the intensity of the modified peptides, each modified peptide in the sample that is a substrate of said protein modifying enzyme, the total number of modified peptides in the sample, the intensity of the modified peptides and all of the modified peptides in the sample. A method of quantifying the activity of a protein modifying enzyme in a sample, comprising calculating the value SC for said protein-modifying enzyme on the basis of a reduction in proliferation using an inhibitor at an inhibitor concentration at which proliferation is measured and the “in vitro” IC50i of the inhibitor against a primary target is also provided. The invention further provides methods of identifying inhibitors with which to treat a patient, methods of treatment, a computer readable medium, a computer program product and devices for carrying out the methods.
Core Innovation
The invention provides a method of treating a patient in need thereof with an inhibitor of a protein-modifying enzyme by using modified-peptide mass spectrometry data to identify and rank protein-modifying enzymes for personalized treatment. The method identifies and/or quantifies modified peptides in a patient sample using mass spectrometry, including adding reference modified peptides, carrying out mass spectrometry to obtain data relating to peptides, and comparing the data with data in a database of modified peptides to identify modified peptides in the sample.
For each protein-modifying enzyme in the patient sample, the method calculates a value K based on modified peptides that are substrates of the protein-modifying enzyme and on the summed intensities of modified peptides. The calculation uses m, l, αi, βj, and the intensities of modified peptides, where the highest value K determines the protein-modifying enzyme selected from a specified set of protein kinases and related kinase groups.
The method then identifies an inhibitor that targets the protein-modifying enzyme with the highest K and administers the inhibitor to the patient at a therapeutically effective amount to treat the patient in a personalized manner. The approach links MS-derived modified-peptide substrate activity patterns to inhibitor selection for personalized treatment.
Claims Coverage
The independent claim covers a complete personalized treatment workflow comprising MS identification/quantification of modified peptides from a patient sample using reference modified peptides and database comparison, calculation of a per-enzyme ranking value K for each protein-modifying enzyme, selection of the protein-modifying enzyme with the highest K from a specified enzyme set, selection of an inhibitor targeting that enzyme, and administration of the inhibitor at a therapeutically effective amount. The inventive features are driven by the definition of the K calculation and the enzyme-targeting selection step.
Mass spectrometry identification of modified peptides using reference modified peptides and a modified-peptide database
Identifying and/or quantifying modified peptides in a sample from the patient using mass spectrometry by adding reference modified peptides, carrying out mass spectrometry on the mixture to obtain data relating to the peptides, and comparing the data relating to the peptides with data in a database of modified peptides to identify modified peptides in the sample.
Kinase activity ranking via calculation of a per-enzyme value K from modified-peptide intensities
Calculating a value K for each protein-modifying enzyme in the sample according to the summation-based K formula using m as the number of modified peptides in the sample that are substrates of the protein-modifying enzyme, α as the intensity of modified peptides i, l as the total number of modified peptides, β as the intensity of modified peptides j, and j as all modified peptides in the sample.
Selecting the protein-modifying enzyme with the highest K from a specified enzyme set
Identifying the protein-modifying enzyme with the highest value K, wherein the protein-modifying enzyme is selected from protein kinase A, protein kinase B, protein kinase C, protein kinase G, tyrosine kinase, tyrosine kinase-like kinase, calcium-dependent protein kinase, calmodulin-dependent protein kinase, the casein kinase 1 group, CMGC group, and homologues of yeast Sterile 7, Sterile 11, and Sterile 20 kinases.
Inhibitor selection targeting the highest-K protein-modifying enzyme and therapeutic administration
Selecting an inhibitor that targets the protein-modifying enzyme with the highest value K, and administering said inhibitor to said patient at a therapeutically effective amount to treat the patient in a personalized manner.
Across the independent claim, the claim coverage is centered on MS-based identification of modified peptides followed by calculation of a per-enzyme ranking value K, selecting the highest-K protein-modifying enzyme from a defined kinase/enzyme set, selecting an inhibitor targeting that enzyme, and administering the inhibitor at a therapeutically effective amount for personalized treatment.
Stated Advantages
Allows personalized treatment by selecting an inhibitor based on MS-derived identification of modified peptides and ranking via the highest value K.
Documented Applications
Treating a patient in need thereof with an inhibitor of a protein-modifying enzyme using a personalized workflow that includes MS identification/quantification of modified peptides, K calculation per enzyme, selection of the highest-K enzyme, inhibitor selection, and administration at a therapeutically effective amount.
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