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

Marie Beatriz Cabral, Celine Joy Dela Cruz, Yumika Sato, Glenn Oyong, Ofelia Rempillo, Maria Cecilia Galvez and Edgar Vallar
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Marie Beatriz Cabral: Environment and RemoTe Sensing Research (EARTH) Laboratory, Department of Physics, College of Science, De La Salle University Manila, 2401 Taft Avenue, Manila 0922, Philippines
Celine Joy Dela Cruz: Environment and RemoTe Sensing Research (EARTH) Laboratory, Department of Physics, College of Science, De La Salle University Manila, 2401 Taft Avenue, Manila 0922, Philippines
Yumika Sato: Environment and RemoTe Sensing Research (EARTH) Laboratory, Department of Physics, College of Science, De La Salle University Manila, 2401 Taft Avenue, Manila 0922, Philippines
Glenn Oyong: Molecular Science Unit Laboratory, Center for Natural Sciences and Ecological Research, De La Salle University, 2401 Taft Avenue, Manila 0922, Philippines
Ofelia Rempillo: Environment and RemoTe Sensing Research (EARTH) Laboratory, Department of Physics, College of Science, De La Salle University Manila, 2401 Taft Avenue, Manila 0922, Philippines
Maria Cecilia Galvez: Environment and RemoTe Sensing Research (EARTH) Laboratory, Department of Physics, College of Science, De La Salle University Manila, 2401 Taft Avenue, Manila 0922, Philippines
Edgar Vallar: Environment and RemoTe Sensing Research (EARTH) Laboratory, Department of Physics, College of Science, De La Salle University Manila, 2401 Taft Avenue, Manila 0922, Philippines

IJERPH, 2022, vol. 19, issue 14, 1-29

Abstract: Polycyclic aromatic hydrocarbons (PAHs) and volatile organic compounds (VOCs) are widespread across the globe, existing in the environment in complex mixtures potentially capable of initiating respiratory illnesses. Here, we use an in silico approach to evaluate the potential pro-inflammatory effects of various carcinogenic PAHs and VOCs through their binding affinity towards the human toll-like receptor 4 (TLR4). For receptors and ligands, RCSB Protein Data Bank and PubChem were used in obtaining their 3D structures, respectively. Autodock Vina was utilized to obtain the best docking poses and binding affinities of each PAH and VOC. Out of the 14 PAHs included in this study, indeno(1,2,3-cd)pyrene, benzo(ghi)perylene, and benzo[a]pyrene had the highest binding affinity values of −10, −9, and −8.9 kcal/mol, respectively. For the VOCs, out of the 10 compounds studied, benzene, 1,4-dichlorobenzene, and styrene had the highest binding affinity values of −3.6, −3.9, and −4.6 kcal/mol, respectively. Compounds with higher affinity than LPS (−4.1 kcal/com) could potentially induce inflammation, while compounds with lower affinity would be less likely to induce an inflammatory response. Meanwhile, molecular dynamics simulation and RMSF statistical analysis proved that the protein, TLR4, stably preserve its conformation despite ligand interactions. Overall, the structure of the TLR4 was considered inflexible.

Keywords: in silico; molecular dynamics; TLR4; PAHs; VOCs; binding affinity (search for similar items in EconPapers)
JEL-codes: I I1 I3 Q Q5 (search for similar items in EconPapers)
Date: 2022
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