Date of Publication
7-8-2022
Document Type
Bachelor's Thesis
Degree Name
Bachelor of Science in Premed Physics
Subject Categories
Physics
College
College of Science
Department/Unit
Physics
Honor/Award
Outstanding Thesis Award
Thesis Advisor
Edgar A. Vallar
Defense Panel Chair
Maria Cecilia D. Galvez
Defense Panel Member
Ofelia T. Rempillo
Glenn G. Oyong
Abstract/Summary
Polycyclic aromatic hydrocarbons (PAHs) and volatile organic compounds (VOCs) are widespread across the globe as they exist in the environment in complex mixtures which could initiate respiratory illnesses. In this paper, the proinflammatory potential of various carcinogenic PAHs and VOCs were evaluated using an in silico approach. For the molecular docking, the structures of the ligands were obtained from PubChem, while the receptor was obtained from RCSB Protein Data Bank. Meanwhile, AutoDock Vina was utilized to obtain the best docking poses, and binding affinity value (kcal/mol) for each PAH and VOC bound to the human toll-like receptor 4 (TLR4). Indeno(1,2,3-cd)pyrene, benzo(ghi)perylene, and benzo[a]pyrene had the highest binding affinity values among the 14 PAHs studied. For the VOCs, benzene,1,4-dichlorobenzene, and styrene had the highest binding affinity with values of -3.6, -3.9, and -4.6 kcal/mol, respectively. Compounds could potentially induce inflammation if the affinities are higher than LPS (-4.1 kcal/mol), while compounds with lower affinity are less likely to cause inflammation. Statistical analysis and RMSF graphs for the molecular dynamics demonstrated that the receptor, TLR4, will maintain its structure despite ligand interactions. Overall, the structure of the TLR4 was considered inflexible.
Keywords: in silico; molecular docking; molecular dynamics; TLR4; PAHs; VOCs; binding affinity; LPS
Abstract Format
html
Language
English
Format
Electronic
Physical Description
[xvi], 130 leaves
Keywords
Polycyclic aromatic hydrocarbons; Volatile organic compounds; Molecular dynamics
Recommended Citation
Cabral, M. D., Dela Cruz, C. J., & Sato, Y. A. (2022). In silico approach in the evaluation of pro-inflammatory potential of polycyclic aromatic hydrocarbons and volatile organic compounds through binding affinity to the human toll-like receptor 4. Retrieved from https://animorepository.dlsu.edu.ph/etdb_physics/18
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Embargo Period
7-12-2022
