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In silico research on Novel Derivatives of N-(Acetylphenyl)-N-Ferrocenylmethyl-3-nitroaniline as DNA Binding Agents: Using Diverse Computational Methods, including Molecular Docking and ADME/Toxicity Assessment

Year 2024, Volume: 8 Issue: 4, 93 - 102, 02.12.2024
https://doi.org/10.33435/tcandtc.1400064

Abstract

This study presents an in silico investigation into the potential DNA binding properties of novel derivatives of N-(Acetylphenyl)-N-Ferrocenylmethylnitroaniline using different computational techniques, including molecular docking and ADME/Toxicity assessment, we explored the interaction between these derivatives and DNA. The results reveal promising candidates with strong binding affinities to DNA, substantiated by robust electrostatic interactions. Furthermore, our study sheds light on the ADME and toxicity profiles of these compounds, providing insights into their pharmacological potential. These findings offer valuable insights into the design and development of DNA-binding agents with potential applications in various biomedical fields.

References

  • [1] W.D. Wilson, R.L. Jones, Intercalating Drugs: DNA Binding and Molecular Pharmacology, (1981) 177–222.
  • [2] B.W.S. Robinson, Recent advances in molecular biological techniques and their relevance to pulmonary research, Thorax. 55 (2000) 329–339.
  • [3] S. Elleuchi, I. Ortiz de Luzuriaga, Á. Sanchez-Gonzalez, X. Lopez, K. Jarraya, M.J. Calhorda, A. Gil, Computational Studies on the Binding Preferences of Molybdenum(II) Phenanthroline Complexes with Duplex DNA. The Important Role of the Ancillary Ligands, Inorg Chem. 59 (2020) 12711–12721.
  • [4] Y.P. Pang, In Silico Drug Discovery: Solving the “Target-rich and Lead-poor” Imbalance Using the Genome-to-drug-lead Paradigm, Clin Pharmacol Ther. 81 (2007) 30–34.
  • [5] Y. OKUNO, <i>In silico</i> Drug Discovery Based on the Integration of Bioinformatics and Chemoinformatics, YAKUGAKU ZASSHI. 128 (2008) 1645–1651.
  • [6] J. Yoo, D. Winogradoff, A. Aksimentiev, Molecular dynamics simulations of DNA–DNA and DNA–protein interactions, Curr Opin Struct Biol. 64 (2020) 88–96.
  • [7] M.R. Karimpour, D. V. Fedorov, A. Tkatchenko, Molecular Interactions Induced by a Static Electric Field in Quantum Mechanics and Quantum Electrodynamics, J Phys Chem Lett. 13 (2022) 2197–2204.
  • [8] D.A. Gschwend, A.C. Good, I.D. Kuntz, Molecular docking towards drug discovery, Journal of Molecular Recognition. 9 (1996) 175–186.
  • [9] X.-J. Lu, Z. Shakked, W.K. Olson, A-form Conformational Motifs in Ligand-bound DNA Structures, J Mol Biol. 300 (2000) 819–840.
  • [10] I.S. Haworth, A.H. Elcock, J. Freeman, A. Rodger, W.G. Richards, Sequence Selective Binding to the DNA Major Groove: Tris(1,10-phenanthroline) Metal Complexes Binding to Poly(dG-dC) and Poly(dA-dT), J Biomol Struct Dyn. 9 (1991) 23–44.
  • [11] C. Sun, T. Tang, H. Uludağ, J.E. Cuervo, Molecular Dynamics Simulations of DNA/PEI Complexes: Effect of PEI Branching and Protonation State, Biophys J. 100 (2011) 2754–2763.
  • [12] A.G. Cherstvy, Electrostatic interactions in biological DNA-related systems, Physical Chemistry Chemical Physics. 13 (2011) 9942.
  • [13] D. Ohlendorf, Electrostatics and flexibility in protein-DNA interactions, Adv Biophys. 20 (1985) 137–151.
  • [14] C.U. Murade, G.T. Shubeita, A fluorescent reporter on electrostatic DNA-ligand interactions, Biomed Opt Express. 13 (2022) 159.
  • [15] T. Kulikova, P. Padnya, I. Shiabiev, A. Rogov, I. Stoikov, G. Evtugyn, Electrochemical Sensing of Interactions between DNA and Charged Macrocycles, Chemosensors. 9 (2021) 347.
  • [16] M.S. Blackledge, C. Melander, Programmable DNA-binding small molecules, Bioorg Med Chem. 21 (2013) 6101–6114.
  • [17] T. Prueksaritanont, C. Tang, ADME of Biologics—What Have We Learned from Small Molecules?, AAPS J. 14 (2012) 410–419.
  • [18] B.M. Rock, R.S. Foti, Pharmacokinetic and Drug Metabolism Properties of Novel Therapeutic Modalities, Drug Metabolism and Disposition. 47 (2019) 1097–1099.
  • [19] F. Anwar, U. Saleem, A.-U. Rehman, B. Ahmad, M. Froeyen, M.U. Mirza, L.Y. Kee, I. Abdullah, S. Ahmad, Toxicity Evaluation of the Naphthalen-2-yl 3,5-Dinitrobenzoate: A Drug Candidate for Alzheimer Disease, Front Pharmacol. 12 (2021).
  • [20] R. Bhandari, G. Khanna, A. Kuhad, Pharmacological insight into potential therapeutic agents for the deadly Covid-19 pandemic, Eur J Pharmacol. 890 (2021) 173643.
  • [21] K.N. Atuah, D. Hughes, M. Pirmohamed, Clinical Pharmacology, Drug Saf. 27 (2004) 535–554.
  • [22] F. De Abreu, F. De Paula, D. Ferreira, V. Nascimento, J. Lopes, A. Santos, M. Santoro, C. Salas, M. Goulart, The Application of DNA-Biosensors and Differential Scanning Calorimetry to the Study of the DNA-Binding Agent Berenil, Sensors. 8 (2008) 1519–1538.
  • [23] G. Liu, T. Chen, X. Zhang, X. Ma, H. Shi, Small molecule inhibitors targeting the cancers, MedComm (Beijing). 3 (2022).
  • [24] M. Frisch, G. Trucks, H. Schlegel, G.S.- Wallingford, U. CT, U. 2009, Gaussian 09; Gaussian, Inc, Gaussian, (2016).
  • [25] C. Chizallet, S. Lazare, D. Bazer-Bachi, F. Bonnier, V. Lecocq, E. Soyer, A.-A. Quoineaud, N. Bats, Catalysis of Transesterification by a Nonfunctionalized Metal−Organic Framework: Acido-Basicity at the External Surface of ZIF-8 Probed by FTIR and ab Initio Calculations, J Am Chem Soc. 132 (2010) 12365–12377.
  • [26] H. Bux, F. Liang, Y. Li, J. Cravillon, M. Wiebcke, J. Caro, Zeolitic Imidazolate Framework Membrane with Molecular Sieving Properties by Microwave-Assisted Solvothermal Synthesis, J Am Chem Soc. 131 (2009) 16000–16001.
  • [27] S.-L. Li, Q. Xu, Metal–organic frameworks as platforms for clean energy, Energy Environ Sci. 6 (2013) 1656–1683.
  • [28] M.C. Buzzeo, R.G. Evans, R.G. Compton, Non-Haloaluminate Room-Temperature Ionic Liquids in Electrochemistry—A Review, ChemPhysChem. 5 (2004) 1106–1120.
  • [29] A. Abo-Hamad, M.A. AlSaadi, M. Hayyan, I. Juneidi, M.A. Hashim, Ionic Liquid-Carbon Nanomaterial Hybrids for Electrochemical Sensor Applications: a Review, Electrochim Acta. 193 (2016) 321–343.
  • [30] M. Shahsavari, S. Tajik, I. Sheikhshoaie, H. Beitollahi, Fabrication of Nanostructure Electrochemical Sensor Based on the Carbon Paste Electrode (CPE) Modified With Ionic Liquid and Fe3O4/ZIF-67 for Electrocatalytic Sulfamethoxazole Detection, Top Catal. 65 (2022) 577–586.
  • [31] O. Trott, A.J. Olson, AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading, J Comput Chem. (2009).
  • [32] M. Coll, J. Aymami, G.A. Van der Marel, J.H. Van Boom, A. Rich, A.H.J. Wang, Molecular structure of the netropsin-d(CGCGATATCGCG) complex: DNA conformation in an alternating AT segment, Biochemistry. 28 (1989) 310–320.
  • [33] T. Lanez, E. Lanez, A Molecular Docking Study of N-Ferrocenylmethylnitroanilines as Potential Anticancer Drugs, International Journal of Pharmacology, Phytochemistry and Ethnomedicine. 2 (2016) 5–12.
  • [34] E. Lanez, L. Bechki, T. Lanez, Computational molecular docking, voltammetric and spectroscopic DNA interaction studies of 9N-(Ferrocenylmethyl)adenine, Chemistry and Chemical Technology. 13 (2019) 11–17.
  • [35] BIOVIA, Dassault Systèmes, Discovery Studio Visualiser, v21.1.1.020289, San Diego: Dassault Systèmes, 2020., (n.d.).
  • [36] E. Harder, W. Damm, J. Maple, C. Wu, M. Reboul, J.Y. Xiang, L. Wang, D. Lupyan, M.K. Dahlgren, J.L. Knight, J.W. Kaus, D.S. Cerutti, G. Krilov, W.L. Jorgensen, R. Abel, R.A. Friesner, OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins, J Chem Theory Comput. 12 (2016) 281–296.
  • [37] G. Magdy, M.A. Shaldam, F. Belal, H. Elmansi, Multi-spectroscopic, thermodynamic, and molecular docking/dynamic approaches for characterization of the binding interaction between calf thymus DNA and palbociclib, Sci Rep. 12 (2022) 14723.
  • [38] R. Rohs, Molecular flexibility in ab initio drug docking to DNA: binding-site and binding-mode transitions in all-atom Monte Carlo simulations, Nucleic Acids Res. 33 (2005) 7048–7057.
  • [39] M. Walker, A.J.A. Harvey, A. Sen, C.E.H. Dessent, Performance of M06, M06-2X, and M06-HF Density Functionals for Conformationally Flexible Anionic Clusters: M06 Functionals Perform Better than B3LYP for a Model System with Dispersion and Ionic Hydrogen-Bonding Interactions, J Phys Chem A. 117 (2013) 12590–12600.
Year 2024, Volume: 8 Issue: 4, 93 - 102, 02.12.2024
https://doi.org/10.33435/tcandtc.1400064

Abstract

References

  • [1] W.D. Wilson, R.L. Jones, Intercalating Drugs: DNA Binding and Molecular Pharmacology, (1981) 177–222.
  • [2] B.W.S. Robinson, Recent advances in molecular biological techniques and their relevance to pulmonary research, Thorax. 55 (2000) 329–339.
  • [3] S. Elleuchi, I. Ortiz de Luzuriaga, Á. Sanchez-Gonzalez, X. Lopez, K. Jarraya, M.J. Calhorda, A. Gil, Computational Studies on the Binding Preferences of Molybdenum(II) Phenanthroline Complexes with Duplex DNA. The Important Role of the Ancillary Ligands, Inorg Chem. 59 (2020) 12711–12721.
  • [4] Y.P. Pang, In Silico Drug Discovery: Solving the “Target-rich and Lead-poor” Imbalance Using the Genome-to-drug-lead Paradigm, Clin Pharmacol Ther. 81 (2007) 30–34.
  • [5] Y. OKUNO, <i>In silico</i> Drug Discovery Based on the Integration of Bioinformatics and Chemoinformatics, YAKUGAKU ZASSHI. 128 (2008) 1645–1651.
  • [6] J. Yoo, D. Winogradoff, A. Aksimentiev, Molecular dynamics simulations of DNA–DNA and DNA–protein interactions, Curr Opin Struct Biol. 64 (2020) 88–96.
  • [7] M.R. Karimpour, D. V. Fedorov, A. Tkatchenko, Molecular Interactions Induced by a Static Electric Field in Quantum Mechanics and Quantum Electrodynamics, J Phys Chem Lett. 13 (2022) 2197–2204.
  • [8] D.A. Gschwend, A.C. Good, I.D. Kuntz, Molecular docking towards drug discovery, Journal of Molecular Recognition. 9 (1996) 175–186.
  • [9] X.-J. Lu, Z. Shakked, W.K. Olson, A-form Conformational Motifs in Ligand-bound DNA Structures, J Mol Biol. 300 (2000) 819–840.
  • [10] I.S. Haworth, A.H. Elcock, J. Freeman, A. Rodger, W.G. Richards, Sequence Selective Binding to the DNA Major Groove: Tris(1,10-phenanthroline) Metal Complexes Binding to Poly(dG-dC) and Poly(dA-dT), J Biomol Struct Dyn. 9 (1991) 23–44.
  • [11] C. Sun, T. Tang, H. Uludağ, J.E. Cuervo, Molecular Dynamics Simulations of DNA/PEI Complexes: Effect of PEI Branching and Protonation State, Biophys J. 100 (2011) 2754–2763.
  • [12] A.G. Cherstvy, Electrostatic interactions in biological DNA-related systems, Physical Chemistry Chemical Physics. 13 (2011) 9942.
  • [13] D. Ohlendorf, Electrostatics and flexibility in protein-DNA interactions, Adv Biophys. 20 (1985) 137–151.
  • [14] C.U. Murade, G.T. Shubeita, A fluorescent reporter on electrostatic DNA-ligand interactions, Biomed Opt Express. 13 (2022) 159.
  • [15] T. Kulikova, P. Padnya, I. Shiabiev, A. Rogov, I. Stoikov, G. Evtugyn, Electrochemical Sensing of Interactions between DNA and Charged Macrocycles, Chemosensors. 9 (2021) 347.
  • [16] M.S. Blackledge, C. Melander, Programmable DNA-binding small molecules, Bioorg Med Chem. 21 (2013) 6101–6114.
  • [17] T. Prueksaritanont, C. Tang, ADME of Biologics—What Have We Learned from Small Molecules?, AAPS J. 14 (2012) 410–419.
  • [18] B.M. Rock, R.S. Foti, Pharmacokinetic and Drug Metabolism Properties of Novel Therapeutic Modalities, Drug Metabolism and Disposition. 47 (2019) 1097–1099.
  • [19] F. Anwar, U. Saleem, A.-U. Rehman, B. Ahmad, M. Froeyen, M.U. Mirza, L.Y. Kee, I. Abdullah, S. Ahmad, Toxicity Evaluation of the Naphthalen-2-yl 3,5-Dinitrobenzoate: A Drug Candidate for Alzheimer Disease, Front Pharmacol. 12 (2021).
  • [20] R. Bhandari, G. Khanna, A. Kuhad, Pharmacological insight into potential therapeutic agents for the deadly Covid-19 pandemic, Eur J Pharmacol. 890 (2021) 173643.
  • [21] K.N. Atuah, D. Hughes, M. Pirmohamed, Clinical Pharmacology, Drug Saf. 27 (2004) 535–554.
  • [22] F. De Abreu, F. De Paula, D. Ferreira, V. Nascimento, J. Lopes, A. Santos, M. Santoro, C. Salas, M. Goulart, The Application of DNA-Biosensors and Differential Scanning Calorimetry to the Study of the DNA-Binding Agent Berenil, Sensors. 8 (2008) 1519–1538.
  • [23] G. Liu, T. Chen, X. Zhang, X. Ma, H. Shi, Small molecule inhibitors targeting the cancers, MedComm (Beijing). 3 (2022).
  • [24] M. Frisch, G. Trucks, H. Schlegel, G.S.- Wallingford, U. CT, U. 2009, Gaussian 09; Gaussian, Inc, Gaussian, (2016).
  • [25] C. Chizallet, S. Lazare, D. Bazer-Bachi, F. Bonnier, V. Lecocq, E. Soyer, A.-A. Quoineaud, N. Bats, Catalysis of Transesterification by a Nonfunctionalized Metal−Organic Framework: Acido-Basicity at the External Surface of ZIF-8 Probed by FTIR and ab Initio Calculations, J Am Chem Soc. 132 (2010) 12365–12377.
  • [26] H. Bux, F. Liang, Y. Li, J. Cravillon, M. Wiebcke, J. Caro, Zeolitic Imidazolate Framework Membrane with Molecular Sieving Properties by Microwave-Assisted Solvothermal Synthesis, J Am Chem Soc. 131 (2009) 16000–16001.
  • [27] S.-L. Li, Q. Xu, Metal–organic frameworks as platforms for clean energy, Energy Environ Sci. 6 (2013) 1656–1683.
  • [28] M.C. Buzzeo, R.G. Evans, R.G. Compton, Non-Haloaluminate Room-Temperature Ionic Liquids in Electrochemistry—A Review, ChemPhysChem. 5 (2004) 1106–1120.
  • [29] A. Abo-Hamad, M.A. AlSaadi, M. Hayyan, I. Juneidi, M.A. Hashim, Ionic Liquid-Carbon Nanomaterial Hybrids for Electrochemical Sensor Applications: a Review, Electrochim Acta. 193 (2016) 321–343.
  • [30] M. Shahsavari, S. Tajik, I. Sheikhshoaie, H. Beitollahi, Fabrication of Nanostructure Electrochemical Sensor Based on the Carbon Paste Electrode (CPE) Modified With Ionic Liquid and Fe3O4/ZIF-67 for Electrocatalytic Sulfamethoxazole Detection, Top Catal. 65 (2022) 577–586.
  • [31] O. Trott, A.J. Olson, AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading, J Comput Chem. (2009).
  • [32] M. Coll, J. Aymami, G.A. Van der Marel, J.H. Van Boom, A. Rich, A.H.J. Wang, Molecular structure of the netropsin-d(CGCGATATCGCG) complex: DNA conformation in an alternating AT segment, Biochemistry. 28 (1989) 310–320.
  • [33] T. Lanez, E. Lanez, A Molecular Docking Study of N-Ferrocenylmethylnitroanilines as Potential Anticancer Drugs, International Journal of Pharmacology, Phytochemistry and Ethnomedicine. 2 (2016) 5–12.
  • [34] E. Lanez, L. Bechki, T. Lanez, Computational molecular docking, voltammetric and spectroscopic DNA interaction studies of 9N-(Ferrocenylmethyl)adenine, Chemistry and Chemical Technology. 13 (2019) 11–17.
  • [35] BIOVIA, Dassault Systèmes, Discovery Studio Visualiser, v21.1.1.020289, San Diego: Dassault Systèmes, 2020., (n.d.).
  • [36] E. Harder, W. Damm, J. Maple, C. Wu, M. Reboul, J.Y. Xiang, L. Wang, D. Lupyan, M.K. Dahlgren, J.L. Knight, J.W. Kaus, D.S. Cerutti, G. Krilov, W.L. Jorgensen, R. Abel, R.A. Friesner, OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins, J Chem Theory Comput. 12 (2016) 281–296.
  • [37] G. Magdy, M.A. Shaldam, F. Belal, H. Elmansi, Multi-spectroscopic, thermodynamic, and molecular docking/dynamic approaches for characterization of the binding interaction between calf thymus DNA and palbociclib, Sci Rep. 12 (2022) 14723.
  • [38] R. Rohs, Molecular flexibility in ab initio drug docking to DNA: binding-site and binding-mode transitions in all-atom Monte Carlo simulations, Nucleic Acids Res. 33 (2005) 7048–7057.
  • [39] M. Walker, A.J.A. Harvey, A. Sen, C.E.H. Dessent, Performance of M06, M06-2X, and M06-HF Density Functionals for Conformationally Flexible Anionic Clusters: M06 Functionals Perform Better than B3LYP for a Model System with Dispersion and Ionic Hydrogen-Bonding Interactions, J Phys Chem A. 117 (2013) 12590–12600.
There are 39 citations in total.

Details

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

Asma Yahiaoui

Nabil Benyza This is me 0000-0003-2641-8264

Amel Messai This is me 0000-0002-0875-8356

Touhami Lanez

Lanez Elhafnaoui 0000-0002-6543-2547

Early Pub Date July 21, 2024
Publication Date December 2, 2024
Submission Date December 6, 2023
Acceptance Date June 8, 2024
Published in Issue Year 2024 Volume: 8 Issue: 4

Cite

APA Yahiaoui, A., Benyza, N., Messai, A., Lanez, T., et al. (2024). In silico research on Novel Derivatives of N-(Acetylphenyl)-N-Ferrocenylmethyl-3-nitroaniline as DNA Binding Agents: Using Diverse Computational Methods, including Molecular Docking and ADME/Toxicity Assessment. Turkish Computational and Theoretical Chemistry, 8(4), 93-102. https://doi.org/10.33435/tcandtc.1400064
AMA Yahiaoui A, Benyza N, Messai A, Lanez T, Elhafnaoui L. In silico research on Novel Derivatives of N-(Acetylphenyl)-N-Ferrocenylmethyl-3-nitroaniline as DNA Binding Agents: Using Diverse Computational Methods, including Molecular Docking and ADME/Toxicity Assessment. Turkish Comp Theo Chem (TC&TC). December 2024;8(4):93-102. doi:10.33435/tcandtc.1400064
Chicago Yahiaoui, Asma, Nabil Benyza, Amel Messai, Touhami Lanez, and Lanez Elhafnaoui. “In Silico Research on Novel Derivatives of N-(Acetylphenyl)-N-Ferrocenylmethyl-3-Nitroaniline As DNA Binding Agents: Using Diverse Computational Methods, Including Molecular Docking and ADME/Toxicity Assessment”. Turkish Computational and Theoretical Chemistry 8, no. 4 (December 2024): 93-102. https://doi.org/10.33435/tcandtc.1400064.
EndNote Yahiaoui A, Benyza N, Messai A, Lanez T, Elhafnaoui L (December 1, 2024) In silico research on Novel Derivatives of N-(Acetylphenyl)-N-Ferrocenylmethyl-3-nitroaniline as DNA Binding Agents: Using Diverse Computational Methods, including Molecular Docking and ADME/Toxicity Assessment. Turkish Computational and Theoretical Chemistry 8 4 93–102.
IEEE A. Yahiaoui, N. Benyza, A. Messai, T. Lanez, and L. Elhafnaoui, “In silico research on Novel Derivatives of N-(Acetylphenyl)-N-Ferrocenylmethyl-3-nitroaniline as DNA Binding Agents: Using Diverse Computational Methods, including Molecular Docking and ADME/Toxicity Assessment”, Turkish Comp Theo Chem (TC&TC), vol. 8, no. 4, pp. 93–102, 2024, doi: 10.33435/tcandtc.1400064.
ISNAD Yahiaoui, Asma et al. “In Silico Research on Novel Derivatives of N-(Acetylphenyl)-N-Ferrocenylmethyl-3-Nitroaniline As DNA Binding Agents: Using Diverse Computational Methods, Including Molecular Docking and ADME/Toxicity Assessment”. Turkish Computational and Theoretical Chemistry 8/4 (December 2024), 93-102. https://doi.org/10.33435/tcandtc.1400064.
JAMA Yahiaoui A, Benyza N, Messai A, Lanez T, Elhafnaoui L. In silico research on Novel Derivatives of N-(Acetylphenyl)-N-Ferrocenylmethyl-3-nitroaniline as DNA Binding Agents: Using Diverse Computational Methods, including Molecular Docking and ADME/Toxicity Assessment. Turkish Comp Theo Chem (TC&TC). 2024;8:93–102.
MLA Yahiaoui, Asma et al. “In Silico Research on Novel Derivatives of N-(Acetylphenyl)-N-Ferrocenylmethyl-3-Nitroaniline As DNA Binding Agents: Using Diverse Computational Methods, Including Molecular Docking and ADME/Toxicity Assessment”. Turkish Computational and Theoretical Chemistry, vol. 8, no. 4, 2024, pp. 93-102, doi:10.33435/tcandtc.1400064.
Vancouver Yahiaoui A, Benyza N, Messai A, Lanez T, Elhafnaoui L. In silico research on Novel Derivatives of N-(Acetylphenyl)-N-Ferrocenylmethyl-3-nitroaniline as DNA Binding Agents: Using Diverse Computational Methods, including Molecular Docking and ADME/Toxicity Assessment. Turkish Comp Theo Chem (TC&TC). 2024;8(4):93-102.

Journal Full Title: Turkish Computational and Theoretical Chemistry


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