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Year 2026, Volume: 10 Issue: 3, 29 - 41

Abstract

References

  • [1] R Siegel, D Naishadham, A Jemal, Cancer statistics, CA: a cancer journal for clinicians 63 (2013) 11–30
  • [2] F Bray, M Laversanne, H Sung, J Ferlay, R L Siegel, I Soerjomataram, A Jemal, Global cancer statistics 2022: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries, CA: a cancer journal for clinicians 74 (2024) 229-263
  • [3] M H Forouzanfar et al, Global, regional, and national comparative risk assessment of 79 behavioural, environmental and occupational, and metabolic risks or clusters of risks, 1990–2015: a systematic analysis for the Global Burden of Disease Study 2015, The Lancet 388 (2016) 1659–1724
  • [4] A Saini, M Kumar, S Bhatt, V Saini, A Malik, Cancer causes and treatments, Int. J. Pharm. Sci. Res 11 (2020) 3121-3134
  • [5] Y Yaseen, A Kubba, W Shihab, L Tahtamouni, Synthesis, docking study, and structureactivity relationship of novel niflumic acid derivatives acting as anticancer agents by inhibiting VEGFR or EGFR tyrosine kinase activities, Pharmacia 69 (2022) 3
  • [6] N Ebrahimi, E Fardi, H Ghaderi, S Palizdar, R Khorram, R Vafadar, M Ghanaatian, F Rezaei-Tazangi, P Baziyar, A Ahmadi, M R Hamblin, Receptor tyrosine kinase inhibitors in cancer, Cellular and Molecular Life Sciences 80 (2023) 104
  • [7] R Roskoski Jr, Src protein–tyrosine kinase structure and regulation, Biochemical and biophysical research communications 324 (2004) 1155-1164
  • [8] B Piperdi, R Perez-Soler, Role of erlotinib in the treatment of non-small cell lung cancer: clinical outcomes in wild-type epidermal growth factor receptor patients, Drugs 72 (2012) 11-19
  • [9] M S Bilal, S A Ejaz, S Zargar, N Akhtar, T A Wani, N Riaz, A T Aborode, F Siddique, N Altwaijry, H M Alkahtani, H I Umar, Computational investigation of 1, 3, 4 oxadiazole derivatives as lead inhibitors of VEGFR 2 in comparison with EGFR: Density functional theory, molecular docking and molecular dynamics simulation studies, Biomolecules 12 (2022) 1612
  • [10] A. K. B. Aljohani et al., Anticancer evaluations of iodoquinazoline substituted with allyl and/or benzyl as dual inhibitors of EGFR WT and EGFR T790M: design, synthesis, ADMET and molecular docking, RSC advances 14(12) (2024) 7964-7980
  • [11] Y Yang, K Yao, M P Repasky, K Leswing, R Abel, B K Shoichet, S V Jerome, Efficient exploration of chemical space with docking and deep learning, Journal of Chemical Theory and Computation 17 (2021) 7106-7119
  • [12] J H Park, Y Liu, M A Lemmon, R Radhakrishnan, Erlotinib binds both inactive and active conformations of the EGFR tyrosine kinase domain, Biochemical Journal 448 (2012) 417
  • [13] K Okamoto, M Ikemori-Kawada, A Jestel, K von König, Y Funahashi, T Matsushima, A Tsuruoka, A Inoue, J Matsui, Distinct binding mode of multikinase inhibitor lenvatinib revealed by biochemical characterization, ACS medicinal chemistry letters 6 (2015) 89-94
  • [14] G Madhavi Sastry, M Adzhigirey, T Day, R Annabhimoju, W Sherman, Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments, Journal of computer-aided molecular design 27 (2013) 221-234
  • [15] Y Hasan, A Al-hamashi, Identification of selisistat derivatives as SIRT1-3 inhibitors by in silico virtual screening, Turkish Computational and Theoretical Chemistry 8 (2023) 1-11
  • [16] R M H Ali, A A Al-Hamashi, Molecular docking, ADMET, molecular dynamic simulation, synthesis, and preliminary antiproliferative study of 1, 2, 4-thiadiazole derivatives as possible histone deacetylase inhibitors, Tropical Journal of Pharmaceutical Research 23 (2024) 1069-1076
  • [17] K J Bowers, E Chow, H Xu, R O Dror, M P Eastwood, B A Gregersen, J L Klepeis, I Kolossvary, M A Moraes, F D Sacerdoti, J K Salmon, Scalable algorithms for molecular dynamics simulations on commodity clusters, Proceedings of the 2006 ACM/IEEE Conference on Supercomputing (2006) 84-es
  • [18] F Ntie-Kang, An in silico evaluation of the ADMET profile of the StreptomeDB database, Springerplus 2 (2013) 1-11
  • [19] F Gygi, E W Draeger, M Schulz, B R De Supinski, J A Gunnels, V Austel, J C Sexton, F Franchetti, S Kral, C W Ueberhuber, J Lorenz, SC’06: Proceedings of the 2006 ACM/IEEE Conference on Supercomputing (2006)
  • [20] N A Alturki, M M Mashraqi, A Alzamami, Y S Alghamdi, A A Alharthi, S A Asiri, S Ahmad, S Alshamrani, In-silico screening and molecular dynamics simulation of drug bank experimental compounds against SARS-CoV-2, Molecules 27 (2022) 4391
  • [21] Z M Mohammed, A A A Al-Hamashi, Molecular Docking, Admet, and Molecular Dynamics Simulation Studies for Molecules with Expected Hdac Inhibition Activity, Gomal Journal of Medical Sciences 22 (2024) 164-172
  • [22] D Frenkel and B Smit, Understanding Molecular Simulation: From Algorithms to Applications (2nd ed) Academic Press (2002)

In Silico Design of EGFR and VEGFR Dual Inhibitor Using Molecular Docking, ADME, and Molecular Dynamics Simulations Studies

Year 2026, Volume: 10 Issue: 3, 29 - 41

Abstract

Many disorders, especially cancer, are linked to the malfunctioning of receptor tyrosine kinases (RTKs), which are essential for controlling cellular functions like differentiation,proliferation, survival, metabolism, and migration.These include the epidermal growth factor receptor (EGFR) and vascular endothelial growth factor receptor (VEGFR), which have shown promise as targets for anti-neoplastic treatments. Gefitinib and erlotinib are examples of EGFRtargeting inhibitors that have been designed to bind competitively to the tyrosine kinase active site, preventing ATP uptake and preventing downstream signaling from the receptor. Tyrosine kinase inhibitors (TKIs) have demonstrated promise in blocking the signaling pathways of cancer cells; nevertheless, the evolution of resistance calls for the creation of new and powerful inhibitors.In this study, new derivatives of erlotinib was emerged using the numerate feature of the Maestro suite software the binding affinity assessed using molecular docking study where compound RM1 show docking score -10.120-8.775 against 4HJO, 3WZE respectively while the docking score for ERLOTINIB against 4HJO and SORAFINEB against 3WZE are -9.000, -7.495 respectively, while dynamic simulations for RM1 exhibited a protein RMSD with 4HJO below 2.8 Å and below 2 Å with 3WZE , and the assessment of ADME properties are done using Qikprop application within maestro software, our future plan is to synthesize these compounds and invitro study biological activities.


In Silico Design of EGFR and VEGFR Dual Inhibitor Using Molecular Docking, ADME, and Molecular Dynamics Simulations Studies

References

  • [1] R Siegel, D Naishadham, A Jemal, Cancer statistics, CA: a cancer journal for clinicians 63 (2013) 11–30
  • [2] F Bray, M Laversanne, H Sung, J Ferlay, R L Siegel, I Soerjomataram, A Jemal, Global cancer statistics 2022: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries, CA: a cancer journal for clinicians 74 (2024) 229-263
  • [3] M H Forouzanfar et al, Global, regional, and national comparative risk assessment of 79 behavioural, environmental and occupational, and metabolic risks or clusters of risks, 1990–2015: a systematic analysis for the Global Burden of Disease Study 2015, The Lancet 388 (2016) 1659–1724
  • [4] A Saini, M Kumar, S Bhatt, V Saini, A Malik, Cancer causes and treatments, Int. J. Pharm. Sci. Res 11 (2020) 3121-3134
  • [5] Y Yaseen, A Kubba, W Shihab, L Tahtamouni, Synthesis, docking study, and structureactivity relationship of novel niflumic acid derivatives acting as anticancer agents by inhibiting VEGFR or EGFR tyrosine kinase activities, Pharmacia 69 (2022) 3
  • [6] N Ebrahimi, E Fardi, H Ghaderi, S Palizdar, R Khorram, R Vafadar, M Ghanaatian, F Rezaei-Tazangi, P Baziyar, A Ahmadi, M R Hamblin, Receptor tyrosine kinase inhibitors in cancer, Cellular and Molecular Life Sciences 80 (2023) 104
  • [7] R Roskoski Jr, Src protein–tyrosine kinase structure and regulation, Biochemical and biophysical research communications 324 (2004) 1155-1164
  • [8] B Piperdi, R Perez-Soler, Role of erlotinib in the treatment of non-small cell lung cancer: clinical outcomes in wild-type epidermal growth factor receptor patients, Drugs 72 (2012) 11-19
  • [9] M S Bilal, S A Ejaz, S Zargar, N Akhtar, T A Wani, N Riaz, A T Aborode, F Siddique, N Altwaijry, H M Alkahtani, H I Umar, Computational investigation of 1, 3, 4 oxadiazole derivatives as lead inhibitors of VEGFR 2 in comparison with EGFR: Density functional theory, molecular docking and molecular dynamics simulation studies, Biomolecules 12 (2022) 1612
  • [10] A. K. B. Aljohani et al., Anticancer evaluations of iodoquinazoline substituted with allyl and/or benzyl as dual inhibitors of EGFR WT and EGFR T790M: design, synthesis, ADMET and molecular docking, RSC advances 14(12) (2024) 7964-7980
  • [11] Y Yang, K Yao, M P Repasky, K Leswing, R Abel, B K Shoichet, S V Jerome, Efficient exploration of chemical space with docking and deep learning, Journal of Chemical Theory and Computation 17 (2021) 7106-7119
  • [12] J H Park, Y Liu, M A Lemmon, R Radhakrishnan, Erlotinib binds both inactive and active conformations of the EGFR tyrosine kinase domain, Biochemical Journal 448 (2012) 417
  • [13] K Okamoto, M Ikemori-Kawada, A Jestel, K von König, Y Funahashi, T Matsushima, A Tsuruoka, A Inoue, J Matsui, Distinct binding mode of multikinase inhibitor lenvatinib revealed by biochemical characterization, ACS medicinal chemistry letters 6 (2015) 89-94
  • [14] G Madhavi Sastry, M Adzhigirey, T Day, R Annabhimoju, W Sherman, Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments, Journal of computer-aided molecular design 27 (2013) 221-234
  • [15] Y Hasan, A Al-hamashi, Identification of selisistat derivatives as SIRT1-3 inhibitors by in silico virtual screening, Turkish Computational and Theoretical Chemistry 8 (2023) 1-11
  • [16] R M H Ali, A A Al-Hamashi, Molecular docking, ADMET, molecular dynamic simulation, synthesis, and preliminary antiproliferative study of 1, 2, 4-thiadiazole derivatives as possible histone deacetylase inhibitors, Tropical Journal of Pharmaceutical Research 23 (2024) 1069-1076
  • [17] K J Bowers, E Chow, H Xu, R O Dror, M P Eastwood, B A Gregersen, J L Klepeis, I Kolossvary, M A Moraes, F D Sacerdoti, J K Salmon, Scalable algorithms for molecular dynamics simulations on commodity clusters, Proceedings of the 2006 ACM/IEEE Conference on Supercomputing (2006) 84-es
  • [18] F Ntie-Kang, An in silico evaluation of the ADMET profile of the StreptomeDB database, Springerplus 2 (2013) 1-11
  • [19] F Gygi, E W Draeger, M Schulz, B R De Supinski, J A Gunnels, V Austel, J C Sexton, F Franchetti, S Kral, C W Ueberhuber, J Lorenz, SC’06: Proceedings of the 2006 ACM/IEEE Conference on Supercomputing (2006)
  • [20] N A Alturki, M M Mashraqi, A Alzamami, Y S Alghamdi, A A Alharthi, S A Asiri, S Ahmad, S Alshamrani, In-silico screening and molecular dynamics simulation of drug bank experimental compounds against SARS-CoV-2, Molecules 27 (2022) 4391
  • [21] Z M Mohammed, A A A Al-Hamashi, Molecular Docking, Admet, and Molecular Dynamics Simulation Studies for Molecules with Expected Hdac Inhibition Activity, Gomal Journal of Medical Sciences 22 (2024) 164-172
  • [22] D Frenkel and B Smit, Understanding Molecular Simulation: From Algorithms to Applications (2nd ed) Academic Press (2002)
There are 22 citations in total.

Details

Primary Language English
Subjects Physical Chemistry (Other)
Journal Section Research Article
Authors

Rusul Ali 0009-0002-0318-8697

Mohammed Kamil Hadi 0000-0001-5257-2332

Halah A. Sahib 0000-0002-4773-3207

Early Pub Date October 27, 2025
Publication Date December 2, 2025
Submission Date February 16, 2025
Acceptance Date July 8, 2025
Published in Issue Year 2026 Volume: 10 Issue: 3

Cite

APA Ali, R., Hadi, M. K., & A. Sahib, H. (2025). In Silico Design of EGFR and VEGFR Dual Inhibitor Using Molecular Docking, ADME, and Molecular Dynamics Simulations Studies. Turkish Computational and Theoretical Chemistry, 10(3), 29-41.
AMA Ali R, Hadi MK, A. Sahib H. In Silico Design of EGFR and VEGFR Dual Inhibitor Using Molecular Docking, ADME, and Molecular Dynamics Simulations Studies. Turkish Comp Theo Chem (TC&TC). October 2025;10(3):29-41.
Chicago Ali, Rusul, Mohammed Kamil Hadi, and Halah A. Sahib. “In Silico Design of EGFR and VEGFR Dual Inhibitor Using Molecular Docking, ADME, and Molecular Dynamics Simulations Studies”. Turkish Computational and Theoretical Chemistry 10, no. 3 (October 2025): 29-41.
EndNote Ali R, Hadi MK, A. Sahib H (October 1, 2025) In Silico Design of EGFR and VEGFR Dual Inhibitor Using Molecular Docking, ADME, and Molecular Dynamics Simulations Studies. Turkish Computational and Theoretical Chemistry 10 3 29–41.
IEEE R. Ali, M. K. Hadi, and H. A. Sahib, “In Silico Design of EGFR and VEGFR Dual Inhibitor Using Molecular Docking, ADME, and Molecular Dynamics Simulations Studies”, Turkish Comp Theo Chem (TC&TC), vol. 10, no. 3, pp. 29–41, 2025.
ISNAD Ali, Rusul et al. “In Silico Design of EGFR and VEGFR Dual Inhibitor Using Molecular Docking, ADME, and Molecular Dynamics Simulations Studies”. Turkish Computational and Theoretical Chemistry 10/3 (October2025), 29-41.
JAMA Ali R, Hadi MK, A. Sahib H. In Silico Design of EGFR and VEGFR Dual Inhibitor Using Molecular Docking, ADME, and Molecular Dynamics Simulations Studies. Turkish Comp Theo Chem (TC&TC). 2025;10:29–41.
MLA Ali, Rusul et al. “In Silico Design of EGFR and VEGFR Dual Inhibitor Using Molecular Docking, ADME, and Molecular Dynamics Simulations Studies”. Turkish Computational and Theoretical Chemistry, vol. 10, no. 3, 2025, pp. 29-41.
Vancouver Ali R, Hadi MK, A. Sahib H. In Silico Design of EGFR and VEGFR Dual Inhibitor Using Molecular Docking, ADME, and Molecular Dynamics Simulations Studies. Turkish Comp Theo Chem (TC&TC). 2025;10(3):29-41.

Journal Full Title: Turkish Computational and Theoretical Chemistry


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