In Silico Characterization of Molecular Interactions of Aviation-Derived Pollutants with Human Proteins: Implications for Occupational and Public Health
Abstract
1. Introduction
2. Methods
2.1. Identification of Target Proteins and Aviation-Derived Air Pollutants
Protein Name | Protein Structure | PDB ID | Normal Function in Cells | Key Health Effects |
---|---|---|---|---|
Estrogen receptor (ER) α ligand-binding domain | 3ERT | Nuclear hormone receptor; ligand-activated transcription factor for estrogen-responsive genes. | Endocrine disruption linked to breast cancer and fertility disorders in exposed populations [17]. | |
Androgen receptor (AR) ligand-binding domain | 2AM9 | Ligand-activated transcription factor controlling male sexual differentiation and reproductive function. | Endocrine disruption affects pubertal development and spermatogenesis [18]. | |
Thyroid hormone receptor β ligand-binding domain | 1N46 | Nuclear receptor for T3; regulates basal metabolism and development via gene transcription. | Exposure to air pollutants is associated with increased risk of thyroid cancer and hypothyroidism [19]. | |
Vitamin D3 receptor ligand-binding domain | 1IE9 | Ligand-activated transcription factor controlling calcium/phosphate homeostasis. | Vitamin D deficiency exacerbates asthma and chronic obstructive pulmonary disorder (COPD) in chronically exposed cohorts [20]. | |
Acetylcholinesterase | 4M0E | Hydrolyzes acetylcholine to terminate neurotransmission at cholinergic synapses. | Structural alterations observed in different types of tumors from the brain, lung, breast, renal, and colon cancers [21]. | |
Human serum albumin (HSA) | 1H9Z | Main plasma carrier for fatty acids, hormones, and drugs; maintains oncotic pressure. | Forms adducts with pollutants like PAHs and is used as a biomarker for pollutant exposure [22]. | |
Hemoglobin (α-chain) | 2DN1 | Transports O2 from lungs to tissues and CO2 back to lungs. | Exposure to air pollutants has been associated with reduced hemoglobin levels and anemia [23]. | |
Cytochrome P450 1A1 (CYP1A1) | 4I8V | Monooxygenase metabolizing xenobiotics (PAHs; drugs) and endogenous lipids. | Impacts pulmonary inflammation due to PAH-induced activity of CYP1A1 [24]. |
2.2. Molecular Docking Simulations
2.3. Determination of Protein–Pollutant Interactions
3. Results and Discussion
3.1. Selection of Pollutants and Proteins for Molecular Docking Analysis
3.2. Binding Affinities of Pollutant–Protein Complexes
3.3. Structural Interactions of High-Affinity Protein–Pollutant Complexes
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
References
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Pollutant Category | Chemical Pollutant | Estrogen Receptor | Androgen Receptor | Thyroid Receptor | Nuclear Receptor Vit D | Acetylcholinesterase | Human Serum Albumin | Hemoglobin Alpha | Cytochrome P450 1A1 | Average Affinity Across Proteins | Average Affinity for Pollutant Category |
---|---|---|---|---|---|---|---|---|---|---|---|
Light chain aliphatic VOCs | Formaldehyde | −1.8 | −1.7 | −1.9 | −2.3 | −2.0 | −2.0 | −1.7 | −1.7 | −1.9 | −3.1 |
Acetaldehyde | −2.6 | −2.6 | −2.6 | −3.0 | −3.0 | −2.6 | −2.3 | −2.5 | −2.6 | ||
Acrolein | −2.8 | −3.3 | −3.2 | −3.2 | −3.1 | −3.3 | −2.8 | −3.3 | −3.1 | ||
Propionaldehyde | −2.9 | −3.2 | −3.3 | −2.8 | −3.0 | −3.4 | −2.9 | −3.4 | −3.1 | ||
1,3-Butadiene | −3.1 | −3.6 | −3.3 | −2.9 | −3.3 | −3.7 | −3.2 | −4.0 | −3.4 | ||
Hexane | −3.8 | −4.0 | −4.2 | −3.4 | −4.1 | −4.5 | −4.1 | −5.0 | −4.1 | ||
Heavy chain aliphatic VOCs | Nonane | −4.4 | −3.8 | −4.8 | −3.8 | −5.0 | −5.6 | −4.5 | −5.9 | −4.7 | −4.7 |
Decane | −4.1 | −3.9 | −3.5 | −3.9 | −5.1 | −5.7 | −4.7 | −6.2 | −4.7 | ||
Nonanal | −4.3 | −4.0 | −4.6 | −3.8 | −5.0 | −5.4 | −3.7 | −5.9 | −4.6 | ||
Decanal | −4.3 | −4.2 | −4.1 | −4.1 | −5.0 | −5.7 | −5.3 | −6.2 | −4.9 | ||
Monoaromatic VOCs | Benzene | −4.2 | −5.0 | −4.5 | −3.7 | −4.9 | −5.2 | −4.4 | −5.6 | −4.7 | −5.5 |
Toluene | −5.0 | −5.0 | −5.2 | −4.3 | −5.5 | −6.1 | −5.3 | −6.4 | −5.3 | ||
Ethylbenzene | −5.0 | −5.0 | −5.2 | −4.5 | −5.7 | −6.5 | −5.5 | −6.8 | −5.5 | ||
o-Xylene | −5.5 | −5.3 | −5.7 | −4.6 | −6.1 | −6.8 | −5.8 | −7.1 | −5.9 | ||
p-Xylene | −5.3 | −5.3 | −5.8 | −4.7 | −5.9 | −6.8 | −5.5 | −7.1 | −5.8 | ||
Styrene | −4.9 | −5.3 | −5.5 | −4.5 | −5.7 | −6.5 | −5.6 | −6.8 | −5.6 | ||
PAHs - two (top) to five (bottom) aromatic rings | Naphthalene | −6.3 | −5.9 | −6.4 | −5.2 | −7.2 | −8.3 | −7.0 | −8.5 | −6.9 | −9.0 |
2-hydroxynaphthalene | −6.2 | −6.1 | −5.6 | −5.3 | −7.0 | −8.3 | −5.7 | −8.8 | −6.6 | ||
Acenaphthene | −6.9 | −7.4 | −7.3 | −5.7 | −8.4 | −9.6 | −8.3 | −9.9 | −7.9 | ||
Fluorene | −7.5 | −7.6 | −6.6 | −5.8 | −8.9 | −10.0 | −7.8 | −10.5 | −8.1 | ||
Acenaphthylene | −6.9 | −7.4 | −8.0 | −5.8 | −8.4 | −9.8 | −8.3 | −9.9 | −8.1 | ||
Phenanthrene | −7.9 | −8.2 | −8.2 | −6.1 | −9.6 | −10.7 | −8.3 | −11.2 | −8.8 | ||
Anthracene | −7.6 | −6.7 | −8.1 | −6.1 | −9.4 | −10.7 | −7.9 | −11.2 | −8.5 | ||
Fluoranthene | −8.4 | −9.0 | −8.0 | −6.8 | −10.2 | −12.0 | −8.6 | −12.6 | −9.5 | ||
Pyrene | −8.2 | −7.6 | −6.9 | −6.7 | −10.5 | −11.8 | −10.4 | −12.3 | −9.3 | ||
Cyclopenta-cd-pyrene | −8.4 | −8.3 | −8.2 | −7.1 | −11.2 | −13.2 | −7.6 | −13.9 | −9.7 | ||
Benzo-a-pyrene | −8.6 | −9.5 | −8.0 | −7.1 | −12.2 | −13.3 | −7.3 | −15.3 | −10.2 | ||
Benzo-g-chrysene | −9.3 | −7.8 | −8.2 | −7.7 | −10.9 | −14.5 | −8.1 | −16.3 | −10.3 | ||
Dibenz-ah-anthracene | −8.8 | −8.3 | −8.3 | −7.8 | −12.6 | −14.0 | −8.0 | −16.3 | −10.5 | ||
Dibenzo-ae-pyrene | −10.1 | −8.6 | −9.4 | −8.0 | −12.2 | −15.0 | −8.4 | −17.6 | −11.1 | ||
Benzo-ghi-perylene | −8.9 | −8.1 | −8.2 | −7.4 | −10.8 | −14.6 | −7.4 | −16.1 | −10.2 | ||
Organophosphate esters | TCP | −7.5 | −7.4 | −7.1 | −6.6 | −8.9 | −9.8 | −6.5 | −9.5 | −7.9 | −6.7 |
TDCIPP | −4.6 | −4.3 | −5.0 | −4.5 | −5.4 | −5.4 | −4.0 | −6.6 | −5.0 | ||
TPHP | −6.9 | −6.5 | −6.5 | −6.5 | −7.3 | −8.7 | −6.3 | −9.5 | −7.3 | ||
Average affinity of protein for all pollutants | -6.0 | −5.9 | −5.9 | −5.2 | −7.2 | −8.2 | −6.0 | −8.8 |
Protein | Ligand | Interaction | Residues |
---|---|---|---|
Estrogen receptor | Benzo-a-pyrene | Hydrophobic interactions | Ala350, Leu354, Trp383, Leu525, Leu536 |
Pi-stacking | Trp383 | ||
Dibenzo-ae-pyrene | Hydrophobic interactions | Thr347, Leu354, Trp383, Leu525, Leu536 | |
Pi-stacking | Trp383 | ||
Tricresyl phosphate | Hydrophobic interactions | Leu354, Trp383, Leu525, Tyr526, Lys529, Val533, Leu536 | |
Pi-stacking | Trp383 | ||
Androgen receptor | Benzo-a-pyrene | Hydrophobic interactions | Leu707, Gln711, Met745, Val746, Leu873 |
Pi-stacking | Phe764 | ||
Dibenzo-ae-pyrene | Hydrophobic interactions | Ile816, Val818, Lys912, Ile914, Tyr915 | |
Tricresyl phosphate | Hydrogen bonds | Trp751 | |
Hydrophobic interactions | Glu681, Pro682, Val684, Ala748, Arg752, Pro801, Phe804, Leu805 | ||
Pi-cation interactions | Arg752 | ||
Thyroid receptor | Benzo-a-pyrene | Hydrophobic interactions | Ile303, Lys306, Ala436, Phe459 |
Dibenzo-ae-pyrene | Hydrophobic interactions | Ile303, Lys306, Ala436, Phe459 | |
Pi-cation interactions | Arg383 | ||
Tricresyl phosphate | Hydrogen bonds | Lys411, His412, Phe417, Trp418 | |
Salt bridges | Lys211 | ||
Hydrophobic interactions | Ile407, Lys411, Trp418 | ||
Pi-cation interactions | Lys211 | ||
Nuclear receptor Vit D | Benzo-a-pyrene | Hydrophobic interactions | Gln364, Arg368, Leu378, Tyr380 |
Dibenzo-ae-pyrene | Hydrophobic interactions | Gln152, Phe153, Tyr236, Thr415 | |
Tricresyl phosphate | Hydrogen bonds | Arg343, Asn394 | |
Hydrophobic interactions | Pro344, Arg391, Asn394, Glu395 | ||
Acetylcholinesterase | Benzo-a-pyrene | Hydrophobic interactions | Tyr72, Trp286, Val294, Phe338, Tyr341 |
Pi-stacking | Trp286, Tyr341 | ||
Dibenzo-ae-pyrene | Hydrophobic interactions | Tyr72, Trp286, Leu289, Phe338, Tyr341 | |
Pi-stacking | Trp286 | ||
Tricresyl phosphate | Hydrophobic interactions | Trp286, Leu289, Glu292, Tyr337, Phe338, Tyr341 | |
Pi-stacking | Tyr341 | ||
Human Serum Albumin (HSA) | Benzo-a-pyrene | Hydrophobic interactions | Arg117, Phe134, Tyr138, Ile142, Ala158, Tyr161, Phe165 |
Pi-stacking | Tyr138, Tyr161 | ||
Dibenzo-ae-pyrene | Hydrophobic interactions | Tyr138, Ile142, Leu154, Tyr161 | |
Pi-stacking | Tyr161 | ||
Tricresyl phosphate | Hydrogen bonds | Tyr161 | |
Hydrophobic interactions | Arg117, Phe134, Tyr138, Ile142, Phe157, Tyr161, Phe165 | ||
Pi-stacking | Tyr138, Tyr161 | ||
Hemoglobin alpha | Benzo-a-pyrene | Hydrophobic interactions | Glu23, Glu27, Glu30, Val55 |
Dibenzo-ae-pyrene | Hydrophobic interactions | Glu23, Ala26, Glu27, Glu30, Val55, Lys56 | |
Tricresyl phosphate | Hydrophobic interactions | Glu23, Ala26, Val55, Lys56 | |
Cytochrome P450 1A1 (CYP 1A1) | Benzo-a-pyrene | Hydrophobic interactions | Phe123, Phe224, Phe258, Ala317, Phe319, Asp320, Thr321, Ile386, Leu496 |
Pi-stacking | Phe224 | ||
Dibenzo-ae-pyrene | Hydrophobic interactions | Ile115, Phe123, Phe224, Phe258, Leu312, Asp313, Ala317, Phe319, Asp320, Thr321, Ile386, Leu496 | |
Pi-stacking | Phe224 | ||
Tricresyl phosphate | Hydrophobic interactions | Ile115, Phe224, Leu254, Phe258, Leu312, Ala317, Phe319, Asp320, Ile386, Leu496 | |
Pi-stacking | Phe123, Phe224 | ||
Hydrogen bonds | Ala317 |
Individual Pollutant Binding Affinity | Multi-Pollutant Binding Affinity | |||||
---|---|---|---|---|---|---|
Protein | VOC (p-xylene) | PAH (Benzo-a-pyrene) | OPE (Tricresyl phosphate) | VOC-PAH | PAH-OPE | VOC-OPE |
Androgen receptor | −5.4 | −10.5 | −7.4 | −16 | −13 | −9.9 |
Human serum albumin | −5.9 | −12.2 | −9 | −19.3 | −18.5 | −14.6 |
Acetylcholinesterase | −6.7 | −13.3 | −10 | −18 | −17.6 | −12.5 |
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Narayanan, C.; Nazarenko, Y. In Silico Characterization of Molecular Interactions of Aviation-Derived Pollutants with Human Proteins: Implications for Occupational and Public Health. Atmosphere 2025, 16, 919. https://doi.org/10.3390/atmos16080919
Narayanan C, Nazarenko Y. In Silico Characterization of Molecular Interactions of Aviation-Derived Pollutants with Human Proteins: Implications for Occupational and Public Health. Atmosphere. 2025; 16(8):919. https://doi.org/10.3390/atmos16080919
Chicago/Turabian StyleNarayanan, Chitra, and Yevgen Nazarenko. 2025. "In Silico Characterization of Molecular Interactions of Aviation-Derived Pollutants with Human Proteins: Implications for Occupational and Public Health" Atmosphere 16, no. 8: 919. https://doi.org/10.3390/atmos16080919
APA StyleNarayanan, C., & Nazarenko, Y. (2025). In Silico Characterization of Molecular Interactions of Aviation-Derived Pollutants with Human Proteins: Implications for Occupational and Public Health. Atmosphere, 16(8), 919. https://doi.org/10.3390/atmos16080919