Refining computer-aided drug design routes for probing difficult protein targets and interfaces

In 2020, cancer impacted an estimated 1.8 million people and result in over 600,000 deaths in the United States. Some cancer treatments options are limited due to drug resistance, requiring additional drug development to improve patient survival rates. It is necessary to continuously develop new therapeutic approaches and identify novel targets, as cancer is ever-growing and adapting. Experimental research strategies have limitations when exploring how to target certain protein classes, including membrane-embedded or protein-protein bound, due to the complexity of their environments. These two domains of research are experimentally challenging to explore, and in silico research practices provide insight that would otherwise take years to study. Computer-aided drug design (CADD) routes can support the areas of drug discovery that are considered difficult to explore with experimental techniques. In this work, we provide research practices that are easily adaptable and translatable to other difficult protein targets and interfaces. First, we identified the morphological impact of a single-site mutation in the G-protein coupled receptor (GPCR), OR2T7, which had been identified as a novel prognostic marker for glioblastoma. Next, we explored the blockbuster target, Programmed Cell Death Protein 1 (PD-1) and the agonistic vs antagonistic response that can be exploited for Non-Small Cell Lung Cancer (NSCLC) therapeutic development. Last, we explored the sphingolipid transport protein, Spns2, which has been demonstrated to be important in regulating the metastatic cancer enabling microenvironment. This work utilized molecular dynamics simulations (MDS) to explore the protein structure-function relationship for each protein of interest, allowing for the exploration of biophysical properties and protein dynamics. We identified that the D125V mutation in OR2T7 likely influences activation of the MAPK pathway by impacting G-protein binding via reducing the helical plasticity in the TM6 and TM7 regions. PD-1 was identified ...