Research Article
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Year 2025, Volume: 9 Issue: 2, 137 - 146, 04.05.2025
https://doi.org/10.33435/tcandtc.1683071

Abstract

References

  • [1] Fokkens, W. J., Lund, V. J., Hopkins, C., et al. European Position Paper on Rhinosinusitis and Nasal Polyps 2020. Rhinology Supplement, 29 (2020) 1–464.
  • [2] Rosenfeld, R. M., Piccirillo, J. F., Chandrasekhar, S. S., Brook, I., Ashok Kumar, K., Kramper, M., ... & Corrigan, M. D. Clinical practice guideline (update): adult sinusitis. Otolaryngology–Head and Neck Surgery, 152(2_suppl) (2015) S1-S39.
  • [3] World Health Organization.. Antibacterial agents in clinical development: an analysis of the antibacterial clinical development pipeline (2020).
  • [4] Livermore, D. M. Beta-lactamases in laboratory and clinical resistance. Clinical Microbiology Reviews, 8(4) (1995) 557–584.
  • [5] Canonica, G. W., Bousquet, J., Mullol, J., Scadding, G. K., & Virchow, J. C. A survey of the burden of allergic rhinitis in Europe. Allergy, 62(Suppl. 85) (2007) 17–25.
  • [6] Pagadala, N. S., Syed, K., & Tuszynski, J. (2017). Software for molecular docking: a review. Biophysical Reviews, 9(2), 91–102.
  • [7] Meng, X. Y., Zhang, H. X., Mezei, M., & Cui, M. Molecular docking: A powerful approach for structure-based drug discovery. Current Computer-Aided Drug Design, 7(2), (2011) 146–157.
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  • [9] Barnes, P. J. Glucocorticosteroids: current and future directions. British Journal of Pharmacology, 163(1) (2011) 29–43.
  • [10] Eccles, R. Substitution of phenylephrine for pseudoephedrine as a nasal decongestant. British Journal of Clinical Pharmacology, 63(1) (2007) 10–14.
  • [11] https://www.dockingserver.com
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  • [13] Stewart, J. J. (2007). Stewart computational chemistry. http://openmopac. net/.
  • [14] Stec, B., Holtz, K. M., Wojciechowski, C. L., & Kantrowitz, E. R. Structure of the wild-type TEM-1 β-lactamase at 1.55 Å and the mutant enzyme Ser70Ala at 2.1 Å suggest the mode of noncovalent catalysis for the mutant enzyme. Biological Crystallography, 61(8) (2005) 1072-1079.
  • [15] Shimamura, T., Shiroishi, M., Weyand, S., Tsujimoto, H., Winter, G., Katritch, V., ... & Iwata, S. Structure of the human histamine H1 receptor complex with doxepin. Nature, 475(7354) (2011) 65-70.
  • [16] Crystal Structure of the Glucocorticoid Receptor Ligand Binding Domain Reveals a Novel Mode of Receptor Dimerization and Coactivator Recognition
  • [17] Cherezov, V., Rosenbaum, D. M., Hanson, M. A., Rasmussen, S. G., Thian, F. S., Kobilka, T. S., ... & Stevens, R. C. High-resolution crystal structure of an engineered human β2-adrenergic G protein–coupled receptor. science, 318(5854) (2007) 1258-1265.
  • [18] Huey, R., Morris, G. M., Olson, A. J., & Goodsell, D. S. A semiempirical free energy force field with charge‐based desolvation. Journal of computational chemistry, 28(6) (2007) 1145-1152.
  • [19] Abdel-Hamid, M. K., & McCluskey, A. In silico docking, molecular dynamics and binding energy insights into the bolinaquinone-clathrin terminal domain binding site. Molecules, 19(5) (2014) 6609-6622.
  • [20] Jung, H. A., Oh, S. H., & Choi, J. S. Molecular docking studies of phlorotannins from Eisenia bicyclis with BACE1 inhibitory activity. Bioorganic & Medicinal Chemistry Letters, 20(11) (2010) 3211-3215.
  • [21] Pagadala, N. S., Syed, K., & Tuszynski, J. Software for molecular docking: a review. Biophysical reviews, 9(2) (2017) 91-102.
  • [22] Jones, S., & Thornton, J. M. Prediction of protein-protein interaction sites using patch analysis. Journal of molecular biology, 272(1) (1997) 133-143.
  • [23] Barnes, C. M., Schaubroeck, J., Huth, M., & Ghumman, S. Lack of sleep and unethical conduct. Organizational Behavior and Human Decision Processes, 115(2) (2011) 169-180.
  • [24] Browne, E. H., Homeopathy–a dilemma for contemporary medicine a quantum therapy misunderstood (2022).
  • [25] Riley, W. J., Subin, Z. M., Lawrence, D. M., Swenson, S. C., Torn, MS, Meng, L., ... & Hess, P. Barriers to predicting changes in global terrestrial methane fluxes: analyses using CLM4Me, a methane biogeochemistry model integrated in CESM. Biogeosciences, 8(7) (2011) 1925-1953.
  • [26] Pagadala, N. S., Syed, K., & Tuszynski, J. Software for molecular docking: a review. Biophysical reviews, 9(2) (2017) 91-102.
  • [27] Heath, K. R., Rogers, R. S., & Fazel, N. Oral manifestations of connective tissue disease and novel therapeutic approaches. Dermatology Online Journal, 21(10) (2015).
  • [28] Eccles, R. Efficacy of phenylephrine. British Journal of Clinical Pharmacology, 64(4) (2007) 557.

Investigation of the Interaction of ENT Drugs with Target Proteins Using a Molecular Docking Approach

Year 2025, Volume: 9 Issue: 2, 137 - 146, 04.05.2025
https://doi.org/10.33435/tcandtc.1683071

Abstract

Understanding the interactions of drugs commonly used in the treatment of Ear, Nose and Throat (ENT) diseases at the molecular level is of great importance in terms of increasing treatment efficacy and identifying new therapeutic targets. In this study, five different active drug substances commonly used in the field of ENT (amoxicillin, loratadine, fluticasone and pseudoephedrine) were selected and the binding potentials of these molecules with the relevant biological target proteins (PDB IDs 1ZG4, 3RZE, 1M2Z, 4V7U, 2RH1) were investigated by molecular docking methods. The selected proteins are associated with bacterial resistance mechanisms, allergic responses, inflammation processes and sympathomimetic effects and play important roles in explaining the therapeutic effects of the relevant drugs. It is aimed that the molecular docking results will contribute to the optimization of drug design and current treatment approaches by revealing the structural basis of drug-protein interactions.

References

  • [1] Fokkens, W. J., Lund, V. J., Hopkins, C., et al. European Position Paper on Rhinosinusitis and Nasal Polyps 2020. Rhinology Supplement, 29 (2020) 1–464.
  • [2] Rosenfeld, R. M., Piccirillo, J. F., Chandrasekhar, S. S., Brook, I., Ashok Kumar, K., Kramper, M., ... & Corrigan, M. D. Clinical practice guideline (update): adult sinusitis. Otolaryngology–Head and Neck Surgery, 152(2_suppl) (2015) S1-S39.
  • [3] World Health Organization.. Antibacterial agents in clinical development: an analysis of the antibacterial clinical development pipeline (2020).
  • [4] Livermore, D. M. Beta-lactamases in laboratory and clinical resistance. Clinical Microbiology Reviews, 8(4) (1995) 557–584.
  • [5] Canonica, G. W., Bousquet, J., Mullol, J., Scadding, G. K., & Virchow, J. C. A survey of the burden of allergic rhinitis in Europe. Allergy, 62(Suppl. 85) (2007) 17–25.
  • [6] Pagadala, N. S., Syed, K., & Tuszynski, J. (2017). Software for molecular docking: a review. Biophysical Reviews, 9(2), 91–102.
  • [7] Meng, X. Y., Zhang, H. X., Mezei, M., & Cui, M. Molecular docking: A powerful approach for structure-based drug discovery. Current Computer-Aided Drug Design, 7(2), (2011) 146–157.
  • [8] Kushwaha, A., & Gupta, P.. Amoxicillin: mechanism of action, pharmacokinetics, and therapeutic implications in bacterial infections. PEXACY International Journal of Pharmaceutical Science, 2(6) (2023) 42-64.
  • [9] Barnes, P. J. Glucocorticosteroids: current and future directions. British Journal of Pharmacology, 163(1) (2011) 29–43.
  • [10] Eccles, R. Substitution of phenylephrine for pseudoephedrine as a nasal decongestant. British Journal of Clinical Pharmacology, 63(1) (2007) 10–14.
  • [11] https://www.dockingserver.com
  • [12] Bikadi, Z., & Hazai, E. Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock. Journal of cheminformatics, 1 (2009) 1-16.
  • [13] Stewart, J. J. (2007). Stewart computational chemistry. http://openmopac. net/.
  • [14] Stec, B., Holtz, K. M., Wojciechowski, C. L., & Kantrowitz, E. R. Structure of the wild-type TEM-1 β-lactamase at 1.55 Å and the mutant enzyme Ser70Ala at 2.1 Å suggest the mode of noncovalent catalysis for the mutant enzyme. Biological Crystallography, 61(8) (2005) 1072-1079.
  • [15] Shimamura, T., Shiroishi, M., Weyand, S., Tsujimoto, H., Winter, G., Katritch, V., ... & Iwata, S. Structure of the human histamine H1 receptor complex with doxepin. Nature, 475(7354) (2011) 65-70.
  • [16] Crystal Structure of the Glucocorticoid Receptor Ligand Binding Domain Reveals a Novel Mode of Receptor Dimerization and Coactivator Recognition
  • [17] Cherezov, V., Rosenbaum, D. M., Hanson, M. A., Rasmussen, S. G., Thian, F. S., Kobilka, T. S., ... & Stevens, R. C. High-resolution crystal structure of an engineered human β2-adrenergic G protein–coupled receptor. science, 318(5854) (2007) 1258-1265.
  • [18] Huey, R., Morris, G. M., Olson, A. J., & Goodsell, D. S. A semiempirical free energy force field with charge‐based desolvation. Journal of computational chemistry, 28(6) (2007) 1145-1152.
  • [19] Abdel-Hamid, M. K., & McCluskey, A. In silico docking, molecular dynamics and binding energy insights into the bolinaquinone-clathrin terminal domain binding site. Molecules, 19(5) (2014) 6609-6622.
  • [20] Jung, H. A., Oh, S. H., & Choi, J. S. Molecular docking studies of phlorotannins from Eisenia bicyclis with BACE1 inhibitory activity. Bioorganic & Medicinal Chemistry Letters, 20(11) (2010) 3211-3215.
  • [21] Pagadala, N. S., Syed, K., & Tuszynski, J. Software for molecular docking: a review. Biophysical reviews, 9(2) (2017) 91-102.
  • [22] Jones, S., & Thornton, J. M. Prediction of protein-protein interaction sites using patch analysis. Journal of molecular biology, 272(1) (1997) 133-143.
  • [23] Barnes, C. M., Schaubroeck, J., Huth, M., & Ghumman, S. Lack of sleep and unethical conduct. Organizational Behavior and Human Decision Processes, 115(2) (2011) 169-180.
  • [24] Browne, E. H., Homeopathy–a dilemma for contemporary medicine a quantum therapy misunderstood (2022).
  • [25] Riley, W. J., Subin, Z. M., Lawrence, D. M., Swenson, S. C., Torn, MS, Meng, L., ... & Hess, P. Barriers to predicting changes in global terrestrial methane fluxes: analyses using CLM4Me, a methane biogeochemistry model integrated in CESM. Biogeosciences, 8(7) (2011) 1925-1953.
  • [26] Pagadala, N. S., Syed, K., & Tuszynski, J. Software for molecular docking: a review. Biophysical reviews, 9(2) (2017) 91-102.
  • [27] Heath, K. R., Rogers, R. S., & Fazel, N. Oral manifestations of connective tissue disease and novel therapeutic approaches. Dermatology Online Journal, 21(10) (2015).
  • [28] Eccles, R. Efficacy of phenylephrine. British Journal of Clinical Pharmacology, 64(4) (2007) 557.
There are 28 citations in total.

Details

Primary Language English
Subjects Molecular Imaging
Journal Section Research Article
Authors

Mansur Doğan 0000-0002-3964-9363

Publication Date May 4, 2025
Submission Date April 24, 2025
Acceptance Date April 25, 2025
Published in Issue Year 2025 Volume: 9 Issue: 2

Cite

APA Doğan, M. (2025). Investigation of the Interaction of ENT Drugs with Target Proteins Using a Molecular Docking Approach. Turkish Computational and Theoretical Chemistry, 9(2), 137-146. https://doi.org/10.33435/tcandtc.1683071
AMA Doğan M. Investigation of the Interaction of ENT Drugs with Target Proteins Using a Molecular Docking Approach. Turkish Comp Theo Chem (TC&TC). May 2025;9(2):137-146. doi:10.33435/tcandtc.1683071
Chicago Doğan, Mansur. “Investigation of the Interaction of ENT Drugs With Target Proteins Using a Molecular Docking Approach”. Turkish Computational and Theoretical Chemistry 9, no. 2 (May 2025): 137-46. https://doi.org/10.33435/tcandtc.1683071.
EndNote Doğan M (May 1, 2025) Investigation of the Interaction of ENT Drugs with Target Proteins Using a Molecular Docking Approach. Turkish Computational and Theoretical Chemistry 9 2 137–146.
IEEE M. Doğan, “Investigation of the Interaction of ENT Drugs with Target Proteins Using a Molecular Docking Approach”, Turkish Comp Theo Chem (TC&TC), vol. 9, no. 2, pp. 137–146, 2025, doi: 10.33435/tcandtc.1683071.
ISNAD Doğan, Mansur. “Investigation of the Interaction of ENT Drugs With Target Proteins Using a Molecular Docking Approach”. Turkish Computational and Theoretical Chemistry 9/2 (May2025), 137-146. https://doi.org/10.33435/tcandtc.1683071.
JAMA Doğan M. Investigation of the Interaction of ENT Drugs with Target Proteins Using a Molecular Docking Approach. Turkish Comp Theo Chem (TC&TC). 2025;9:137–146.
MLA Doğan, Mansur. “Investigation of the Interaction of ENT Drugs With Target Proteins Using a Molecular Docking Approach”. Turkish Computational and Theoretical Chemistry, vol. 9, no. 2, 2025, pp. 137-46, doi:10.33435/tcandtc.1683071.
Vancouver Doğan M. Investigation of the Interaction of ENT Drugs with Target Proteins Using a Molecular Docking Approach. Turkish Comp Theo Chem (TC&TC). 2025;9(2):137-46.

Journal Full Title: Turkish Computational and Theoretical Chemistry


Journal Abbreviated Title: Turkish Comp Theo Chem (TC&TC)