Computer-assisted modeling for treatment design

Abstract

Some embodiments include a computer-assisted method of biomedical treatment design. For example, a computer system can select a compound model associated with a candidate compound that is structured to bind to a biological target to modulate the biological target into achieving a therapeutic effect. The computer system can then identify a structural feature in the compound model as a hinge region that connects domains in the candidate compound. The computer system then determines a mutation process to introduce a mutation at the hinge region such that the mutation activates the candidate compound. The computer system then generates an updated compound model based on the mutation added to the candidate compound to present in a treatment design interface.

What is claimed is: 
     
         1 . A computer-assisted method for designing biomedical treatment, comprising:
 selecting a compound model associated with a candidate compound that is structured to bind to a biological target to modulate the biological target into achieving a therapeutic effect;   identifying a structural feature in the compound model as a hinge region that connects domains in the candidate compound;   determining a mutation process to introduce a mutation at the hinge region such that the mutation activates the candidate compound, wherein said determining is by matching the structural feature against a hinge region database storing at least an association between the mutation process and the structural feature;   generating an updated compound model based on the mutation added to the candidate compound to present in a treatment design interface; and   presenting the updated compound model as a lead candidate compound for a biomedical treatment.   
     
     
         2 . The computer-assisted method of  claim 1 , wherein the candidate compound is selected from a set of potential compounds identified to have a requisite characteristic corresponding to an ability to bind with the biological target. 
     
     
         3 . The computer-assisted method of  claim 1 , further comprising:
 generating a treatment plan including the mutation process; and   presenting the treatment plan via the treatment design interface.   
     
     
         4 . The computer-assisted method of  claim 1 , wherein generating the mutation process includes designing the mutation process to occur during the biomedical treatment;
 and wherein the mutation process is capable of creating a functional compound according to the updated compound model during the biomedical treatment without pre-making, pre-purifying, or pre-freezing the functional compound before the biomedical treatment.   
     
     
         5 . The computer-assisted method of  claim 4 , wherein the functional compound is an enzyme for a cell therapy or a binding protein for a gene activation therapy. 
     
     
         6 . The computer-assisted method of  claim 1 , wherein said determining the mutation process includes identifying one or more available mutations that are associated with the structural feature in the hinge region database. 
     
     
         7 . The computer-assisted method of  claim 6 , wherein said determining further includes selecting the mutation from among the available mutations that is feasible to be introduced according to structure characteristics of the compound model. 
     
     
         8 . The computer-assisted method of  claim 6 , wherein said determining further includes selecting the mutation from among the available mutations that is capable of activating a functional region of the candidate compound by structurally opening up the domains, wherein the functional region is a region in at least one of the domains that is able to bind to the biological target. 
     
     
         9 . The computer-assisted method of  claim 1 , further comprising:
 determining a free peptide model that is capable of binding to the hinge region to deactivate the candidate compound; and   presenting the free peptide model via the treatment design interface.   
     
     
         10 . The computer-assisted method of  claim 9 , further comprising determining a synthesis process to create a free peptide molecule corresponding to the free peptide model. 
     
     
         11 . The computer-assisted method of  claim 9 , wherein determining the free peptide model includes computing the free peptide model based on the structural feature of the hinge region. 
     
     
         12 . The computer-assisted method of  claim 1 , wherein the biological target is a protein structure, a cellular structure, a gene structure, a microbe feature, or any combination thereof. 
     
     
         13 . The computer-assisted method of  claim 1 , wherein the candidate compound is a synthetic drug or an biological molecule present in living bodies. 
     
     
         14 . A computer-assisted method of building a compound optimization database comprising:
 identifying, via a computer system, a structural feature in a compound model of a functional compound as a hinge region that connects domains in the functional compound;   receiving test data associated with the hinge region of the functional compound via a treatment design interface of the computer system;   determining an activation behavior associated with the hinge region based on the test data; and   associating the structural feature with the activation behavior and the compound model in a hinge region database; and   indexing the hinge region database to configure one or more biomedical treatment plans including a biomedical treatment session to modify a specific hinge region of a candidate compound to activate the candidate compound based on the hinge region database.   
     
     
         15 . The computer-assisted method of  claim 14 , further comprising generating the compound model for the functional compound in the computer system. 
     
     
         16 . The computer-assisted method of  claim 14 , further comprising modeling a mutation at the hinge region associated with the compound model such that the mutation activates the functional compound when introduced to the functional compound. 
     
     
         17 . The computer-assisted method of  claim 14 , wherein the test data includes experimental result of a mutation introduced to a test compound having the structural feature; and wherein said associating includes associating the mutation with the structural feature in the hinge region database. 
     
     
         18 . The computer-assisted method of  claim 14 , wherein the test data includes a size measurement of an amino acid structure in the hinge region. 
     
     
         19 . The computer-assisted method of  claim 18 , wherein determining the activation behavior includes estimating a level of activation during the biomedical treatment session based on the size measurement of the amino acid structure in the hinge region. 
     
     
         20 . A computing device comprising:
 a data storage memory storing executable instructions;   a processor that, when configured by the executable instructions, is operable to execute a process including:
 selecting a compound model associated with a candidate compound that is structured to bind to a biological target to modulate the biological target into achieving a therapeutic effect; 
 identifying a structural feature in the compound model as a hinge region that connects domains in the candidate compound; 
 determining a mutation process to introduce a mutation at the hinge region such that the mutation activates the candidate compound, wherein said determining is by matching the structural feature against a hinge region database; and 
 generating an updated compound model based on the mutation added to the candidate compound to present in a treatment design interface, wherein the updated compound model is presented as a lead candidate compound for a biomedical treatment.