Biophysical insights into dietary antioxidants as cyclooxygenase modulators
Creators: name: Liang, Julia
Publisher: name: RMIT University
Year: 2024
Subjects: classificationCode: 340402
subject: Biomolecular modelling and design

description: Non-steroidal anti-inflammatory drugs (NSAIDs) are among the most widely used therapeutic agents around the world, commonly used to reduce pain. These work by targeting cyclooxygenase (COX) enzymes, which are responsible for the production of inflammatory mediators. There are adverse effects with the use of NSAIDs, including gastrointestinal bleeding, renal disease, and cardiovascular effects. Hence, there has been a rise in the development of alternatives to traditional NSAIDs. Olive oil is a main component of the Mediterranean diet, and is reputable as part of a healthy lifestyle. Phenolic compounds derived from Olea europaea contribute to the antioxidant, anti-microbial, and anti-inflammatory properties of extra virgin olive oil. However, specific mechanisms of action are not yet clear. A previous study found that oleocanthal (OLEO), a phenolic compound derived from the olive, had similar effects to ibuprofen, a commonly used NSAID. There are a multitude of additional compounds in the olive that have yet to be investigated. In this project, it was sought to identify potential olive derived compounds with the ability to inhibit COX enzymes to be used in anti-inflammatory therapeutics. The mechanisms of COX inhibition were also studied using in silico approaches. Following a literature review on COX proteins and olive compounds in Chapter 1, a description of computational theory surrounding the in silico methods employed in this thesis are presented in Chapter 2. In Chapter 3, a comprehensive literature search was performed to create a library of olive compounds, focussing on the class of phenolics for the purpose of this project. The structure of human COX-1 was constructed using homology modelling methods in Chapter 4, followed by virtual screening of the olive phenolic library using molecular docking to determine the COX inhibitory potential of all identified ligands. From the docking study, it was determined that 1-oleyltyrosol (1OL) and ligstroside derivative 2 (LG2) demonstrated the greatest binding affinity to both COX-1 and COX-2. Further screening of the compound library was performed by analysing their biological availability in Chapter 5. From examination of absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties of the library, a novel phenolic compound—methyl malate-β-hydoxytyrosol ester (MMHTE)—was found to both fulfil ADMET criteria and demonstrate strong binding to COX-1 and COX-2. These phenolic compounds were selected for further analysis using molecular dynamics simulations. To complement the ADMET data, a preliminary study on membrane permeability was performed. This was conducted using steered MD simulations of these compounds through a 1,2-dioleyl-sn-glycero-3-phosphocholine (DOPC) lipid bilayer, followed by umbrella sampling simulations of OLEO and MMHTE to estimate the free energy of membrane permeation. Chapter 6 presents a detailed study on the mechanisms of COX inhibition by these selected compounds using MD simulations. Classical MD simulations were carried out on COX-1 and COX-2 complexed with 1OL, LG2, OLEO, MMHTE, as well as their native ligands that were present in the crystal structure. The stability and backbone fluctuation of these complexes were determined. Protein dynamics were examined using essential dynamics methods and network analysis, which identified that the N-terminal epidermal growth factor-like domain and membrane bound domains of COX-1 and -2 exhibited altered motions when ligands were bound. Distinct dynamical modules were identified, as well as the finding that COX-2 inter-residue communications were more sensitive to ligand binding compared to COX-1. The residue contributions to binding free energy were computed using Molecular Mechanics-Poisson Boltzmann Surface Area (MM-PPBSA) methods. Through this research, novel olive phenolic compounds were identified which may possess COX inhibitory properties. Future work may provide additional details of the mechanism of COX inhibition, as well as the synthesis of these novel compounds for in vitro and in vivo validation. Furthermore, it may be demonstrated that olive-derived compounds present a possible avenue for the development of more effective and safe therapeutics in inflammation, as well as provide mechanisms for the anti-inflammatory effects of low dosage dietary COX inhibitors.