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

dc.contributor.authorSharp, Amanda Kristineen
dc.contributor.committeechairBrown, Anne M.en
dc.contributor.committeememberLemkul, Justin Alanen
dc.contributor.committeememberAnandakrishnan, Ramamoorthyen
dc.contributor.committeememberAllen, Kylie Dawnen
dc.contributor.departmentGenetics, Bioinformatics, and Computational Biologyen
dc.date.accessioned2023-06-09T08:00:39Zen
dc.date.available2023-06-09T08:00:39Zen
dc.date.issued2023-06-08en
dc.description.abstractIn 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 to have a domain near the PD-L1 binding interface that increases β-sheet stability and increases residue-residue distances with the membrane-proximal region within PD-1, thus leading to an active conformation. Lastly, Spns2 was identified to follow a rocker-switch transport model and provided preliminary insight into sphingolipid-Spns2 channel binding, interacting with residues Thr216, Arg227, and Met230, as well as highlighting the role of Arg119 in a salt-bridge network of interactions essential in substrate translocation. Collectively, this work illustrates the advantages of computational workflows in the drug discovery process and provides a framework that can be applied for additional GCPRs, transport proteins, or protein-protein interfaces to enhance and accelerate the CADD research.en
dc.description.abstractgeneralCancer is an ever-evolving disease that requires continuous development of new treatment options. Experimental research strategies can be timely, expensive, or lack atomistic insight into drug development processes. Computer-aided drug design (CADD) routes provide research strategies to support areas of drug discovery that can be difficult to explore with experimental techniques. Membrane-bound proteins and protein-protein interfaces are two domains of research that are typically difficult to explore, and computational research practices provide insight that would otherwise take years to study. In this work, we provide research practices that are easily adaptable and translatable to other difficult protein targets and interfaces. First, we identified the 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 active vs inactive states 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 metastatic cancer growth. 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 movement. We identified that the D125V mutation in OR2T7 likely influences activation of the MAPK pathway, which supports multiple cancer-regulation pathways, by impacting G-protein binding via reducing the structural flexibility. PD-1 was identified to have a domain near the PD-L1 binding interface that increases structural stability, thus leading to an upregulation of cancer survival pathways. Lastly, Spns2 analysis provided insight into movement involved in sphingolipid transport, provided preliminary insight into sphingolipid-Spns2 binding, as well as highlighting the role of Arg119 in a network of interactions essential in substrate translocation. Collectively, this work highlights the usefulness of computational workflows in the drug discovery process and provides a framework that can be utilized for additional GPCRs, transport proteins, or protein-protein interfaces to enhance and accelerate the CADD research.en
dc.description.degreeDoctor of Philosophyen
dc.format.mediumETDen
dc.identifier.othervt_gsexam:37087en
dc.identifier.urihttp://hdl.handle.net/10919/115385en
dc.language.isoenen
dc.publisherVirginia Techen
dc.rightsIn Copyrighten
dc.rights.urihttp://rightsstatements.org/vocab/InC/1.0/en
dc.subjectDrug Discoveryen
dc.subjectMolecular Dynamicsen
dc.subjectComputer-Aided Drug Designen
dc.subjectMolecular Modelingen
dc.titleRefining computer-aided drug design routes for probing difficult protein targets and interfacesen
dc.typeDissertationen
thesis.degree.disciplineGenetics, Bioinformatics, and Computational Biologyen
thesis.degree.grantorVirginia Polytechnic Institute and State Universityen
thesis.degree.leveldoctoralen
thesis.degree.nameDoctor of Philosophyen

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