A Novel Process to Efficiently Identify Functional Pathways by Building an Interactome for Refined Drug Target Selection

Overview

Interactomes provide a framework for mapping the cellular interactions that drive essential biological processes, revealing how their disruption leads to diseases like cancer. Analysis of such pathways enables more precise identification of therapeutic drug targets with fewer side effects for patients. Traditionally, interactomes were identified one protein at a time, an arduous task that takes many years to establish a few connections. My novel process is a more efficient and cost-effective method to build interactomes of direct protein interactions and can become increasingly complex as more generations are used to build the interactome. Using p53 as a test case, I performed hierarchical clustering to identify genes co-expressed with p53. A matrix of potential protein interactions between p53 and its co-expressed proteins was generated. Using AlphaFold3 AI modeling, the potential interactions of this matrix were screened for direct protein-protein interactions. This process was repeated for each subsequent generation of direct protein partners identified, resulting in the screening of 10,172 potential protein partners to identify the 124 direct interactions that formed the basis of my p53 interactome. The functional pathways were then mapped by walking the pathways protein-by-protein through the interactome to identify the most likely pathway based on GO terms and published literature. This interactome was quantitatively shown to become more complex and orderly with each generation, suggesting it can convey higher levels of biological information. The 4 functional pathways mapped for p53 (DNA damage response, apoptosis, cell cycle control, and metabolism) included proteins known to be associated with p53. Furthermore, when functionally categorized, the proteins in the interactome represented 13 functions, of which p53 has been shown to be involved in all. Interestingly, trimeric complexes that overlap multiple pathways were also identified, which may serve as molecular switches. Currently, there is no standardized method for identifying molecular switches because they are so difficult to detect; however, this method identified a potential switch that may regulate the convergence or divergence of 3 different critical functional pathways. Using my novel process, researchers can better pinpoint proteins directly and uniquely involved in the functions they aim to regulate by identifying functional biological pathways and pathway hubs. This offers promising drug targets with greater specificity and reduced downstream side effects for patients.

Competition history

• CSEF 2026 Biochemistry/ Molecular Biology (Senior Division) · Entry S-04-28

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