Control Molecule Subsets for Combinatorial Biological Network Modulation
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Solution Overview
Problem
Current methods for developing combinatorial therapies face challenges in identifying effective combinations of control molecules to modulate multiple endogenous targets, due to the complexity of biological networks and the 'combinatorial explosion' of possible drug interactions, leading to inefficient and often ineffective treatment strategies.
Innovation Solution
A method and system for determining a subset of control molecules that act on overlapping targets to produce a biological effect, using a computer-based approach to search for optimal combinations within biological systems, mimicking the many-to-many control structure found in natural biological networks, and employing algorithms like stack sequential or genetic algorithms to identify effective control subsets.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If traditional empirical approaches are used to identify therapeutic combinations, then the process is simple to implement, but the efficiency and effectiveness are poor due to combinatorial explosion
Solution Approach 1:
The patent segments the complex biological network into two distinct layers: a controller layer containing a limited number of control molecules (transcription factors, microRNAs, protein kinases) and a target layer containing the endogenous molecules they regulate. This segmentation reduces the combinatorial explosion by focusing on interactions between these segmented layers rather than all possible molecule combinations.
Solution Approach 2:
The patent transitions from considering all possible drug combinations (a high-dimensional search space) to searching within a constrained controller layer that has been pre-selected based on biological network principles. This dimensional reduction transforms the search problem from examining all possible combinations to examining combinations within a biologically relevant subset.
2Device complexity
If the number of control molecules is reduced to manage complexity, then the search space is simplified, but the ability to modulate multiple targets effectively is compromised
Solution Approach 1:
The patent identifies control molecules that possess multi-functionality, where each control molecule can regulate multiple target molecules across different biological pathways. This allows a smaller number of control molecules to achieve comprehensive modulation of the target layer, maintaining versatility while reducing complexity.
Solution Approach 2:
The patent combines the regulatory functions of multiple control molecules into integrated control sets. By merging the effects of multiple controllers that share common targets or act in coordinated pathways, the system achieves enhanced modulation capability with a reduced number of individual control molecules.
3Measurement precision
If comprehensive screening of all drug combinations is performed, then thoroughness is improved, but the time and computational resources required increase exponentially
Solution Approach 1:
The patent performs preliminary action by pre-identifying and curating a controller layer of molecules based on established biological network knowledge before beginning the combinatorial screening. This preliminary selection filters out irrelevant combinations in advance, allowing thorough screening to be performed only on biologically plausible controller-target interactions rather than all possible drug combinations.
Data Source
AI summary
Methods and systems for determining a set of control molecules for use in a combinatorial approach for the treatment of medical conditions, including providing one or more sets of control molecules, where each control molecule within the set acts on a set of targets and the number of control molecules within the one or more sets of control molecules is fewer than the number of targets within the sets of targets; and searching within the sets of control molecules to identify a subset of control molecules that together with a subset of targets form an artificial system to produce a biological effect through the modulation of the subset of targets.