Araştırma Makalesi
Yıl 2024,
Cilt: 52 Sayı: 2, 129 - 138, 01.04.2024
Öz
In this study, the interaction between the 12 indole-bearing azo compounds (a-l), which were previously synthesized by our research group, and two proteins, 2XIR and 5TGZ, was investigated using an in silico method. The ligand-protein interaction parameters and quantities were determined via molecular docking simulation studies. Since compound e has the lowest docking scores for both 2XIR and 5TGZ, it was selected for additional research on binding interactions. Both e-2XIR and e-5TGZ had docking scores that were lower than those of the control molecules. ADMET characteristics (absorption, distribution, metabolism, excretion, and toxicity) were anticipated using the ADMETlab 2.0 and ProTox-II server. Compound b was categorized as having the greatest levels of toxicity, falling into the sixth toxicity class.
Anahtar Kelimeler
Kaynakça
- F. de Sa Alves, E. Barreiro, C. Manssour Fraga, From Nature to Drug Discovery: The Indole Scaffold as a “Privileged Structure,” Mini Rev. Med. Chem., 9 (2009) 782–793.
- P.F. Lamie, J.N. Philoppes, Design, synthesis, stereochemical determination, molecular docking study, in silico pre-ADMET prediction and anti-proliferative activities of indole-pyrimidine derivatives as Mcl-1 inhibitors, Bioorg. Chem., 116 (2021) 105335.
- H. Abdel-Gawad, H.A. Mohamed, K.M. Dawood, F.A.-R. Badria, Synthesis and Antiviral Activity of New Indole-Based Heterocycles, Chem. Pharm. Bull (Tokyo)., 58 (2010) 1529–1531.
- Y. Li, H. Wu, L. Tang, C. Feng, J. Yu, Y. Li, Y. Yang, B. Yang, Q. He, The potential insulin sensitizing and glucose lowering effects of a novel indole derivative in vitro and in vivo, Pharmacol. Res., 56 (2007) 335–343.
- M.S. Estevão, L.C. Carvalho, D. Ribeiro, D. Couto, M. Freitas, A. Gomes, L.M. Ferreira, E. Fernandes, M.M.B. Marques, Antioxidant activity of unexplored indole derivatives: Synthesis and screening, Eur. J. Med. Chem., 45 (2010) 4869–4878.
- S. Battaglia, E. Boldrini, F. Da Settimo, G. Dondio, C. La Motta, A.M. Marini, G. Primofiore, Indole amide derivatives: synthesis, structure–activity relationships and molecular modelling studies of a new series of histamine H1-receptor antagonists, Eur. J. Med. Chem., 34 (1999) 93–105.
- M.A.A. Radwan, E.A. Ragab, N.M. Sabry, S.M. El-Shenawy, Synthesis and biological evaluation of new 3-substituted indole derivatives as potential anti-inflammatory and analgesic agents, Bioorg. Med. Chem., 15 (2007) 3832–3841.
- A.Y. Alzahrani, Y.A. Ammar, M.A. Salem, M. Abu‐Elghait, A. Ragab, Design, synthesis, molecular modeling, and antimicrobial potential of novel 3‐[(1H ‐pyrazol‐3‐yl)imino]indolin‐2‐one derivatives as DNA gyrase inhibitors, Arch. Pharm (Weinheim)., 355 (2022) e2100266.
- S. Ghanei-Nasab, M. Khoobi, F. Hadizadeh, A. Marjani, A. Moradi, H. Nadri, S. Emami, A. Foroumadi, A. Shafiee, Synthesis and anticholinesterase activity of coumarin-3-carboxamides bearing tryptamine moiety, Eur. J. Med. Chem., 121 (2016) 40–46.
- S. Dadashpour, S. Emami, Indole in the target-based design of anticancer agents: A versatile scaffold with diverse mechanisms, Eur. J. Med. Chem., 150 (2018) 9–29.
- H. Sachdeva, J. Mathur, A. Guleria, Indole Derivatives as Potential Anticancer Agents: A Review, J. Chil. Chem. Soc., 65 (2020) 4900–4907.
- K. Kaur, V. Jaitak, Recent Development in Indole Derivatives as Anticancer Agents for Breast Cancer, Anticancer Agents Med. Chem., 19 (2019) 962–983.
- W. Cui, A. Aouidate, S. Wang, Q. Yu, Y. Li, and S. Yuan, Discovering Anti-Cancer Drugs via Computational Methods, Front Pharmacol., 11 (2020) 733.
- M. H. Baig, K. Ahmad, G. Rabbani, M. Danishuddin, and I. Choi, Computer Aided Drug Design and its Application to the Development of Potential Drugs for Neurodegenerative Disorders, Curr Neuropharmacol., 16 (2018) 740–748.
- H. M. Patel et al., “Design and synthesis of VEGFR-2 tyrosine kinase inhibitors as potential anticancer agents by virtual based screening,” RSC Adv, 5(2015) 56724–56771.
- R. Hanachi et al., “Structural, QSAR, machine learning and molecular docking studies of 5-thiophen-2-yl pyrazole derivatives as potent and selective cannabinoid-1 receptor antagonists,” New Journal of Chemistry, 45 (2021) 17796–17807.
- Ç. Karabacak, Ö. Dilek, Synthesis, solvatochromic properties and theoretical calculation of some novel disazo indole dyes, J. Mol. Liq., 199 (2014) 227–236.
- A. Daina, O. Michielin, V. Zoete, SwissTargetPrediction: updated data and new features for efficient prediction of protein targets of small molecules, Nucleic Acids Res., 47 (2019) W357–W364.
- 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., 31 (2010) 455–461.
- E.F. Pettersen, T.D. Goddard, C.C. Huang, G.S. Couch, D.M. Greenblatt, E.C. Meng, T.E. Ferrin, UCSF Chimera—A visualization system for exploratory research and analysis, J. Comput. Chem., 25 (2004) 1605–1612.
- BIOVIA (2021) Discovery Studio Visualizer, version 21.1.0.20298. Dassault Systèmes, San Diego, CA.
- B. Webb, A. Sali, Comparative Protein Structure Modeling Using MODELLER, Curr. Protoc. Bioinformatics, 54 (2016) 5.6.1-5.6.37.
- S. Russo, W.F. De Azevedo, Advances in the Understanding of the Cannabinoid Receptor 1 – Focusing on the Inverse Agonists Interactions, Curr. Med. Chem., 26 (2019) 1908–1919.
- Ç. Karabacak Atay, Ö. Dilek, T. Tilki, B. Dede, A novel imidazole-based azo molecule: synthesis, characterization, quantum chemical calculations, molecular docking, molecular dynamics simulations and ADMET properties, J. Mol. Model., 29 (2023) 226.
- M.D. Hanwell, D.E. Curtis, D.C. Lonie, T. Vandermeersch, E. Zurek, G.R. Hutchison, Avogadro: an advanced semantic chemical editor, visualization, and analysis platform, J. Cheminform., 4 (2012) 17.
- G. Xiong, Z. Wu, J. Yi, L. Fu, Z. Yang, C. Hsieh, M. Yin, X. Zeng, C. Wu, A. Lu, X. Chen, T. Hou, D. Cao, ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties, Nucleic Acids Res., 49 (2021) W5–W14.
- P. Banerjee, A.O. Eckert, A.K. Schrey, R. Preissner, ProTox-II: a webserver for the prediction of toxicity of chemicals, Nucleic Acids Res., 46 (2018) W257–W263.
- R. Hanachi, R. Ben Said, H. Allal, S. Rahali, M.A.M. Alkhalifah, F. Alresheedi, B. Tangour, M. Hochlaf, Structural, QSAR, machine learning and molecular docking studies of 5-thiophen-2-yl pyrazole derivatives as potent and selective cannabinoid-1 receptor antagonists, New J. Chem., 45 (2021) 17796–17807.
- G.S. Amato, A. Manke, D.L. Harris, R.W. Wiethe, V. Vasukuttan, R.W. Snyder, T.W. Lefever, R. Cortes, Y. Zhang, S. Wang, S.P. Runyon, R. Maitra, Blocking Alcoholic Steatosis in Mice with a Peripherally Restricted Purine Antagonist of the Type 1 Cannabinoid Receptor, J. Med. Chem., 61 (2018) 4370–4385.
Yıl 2024,
Cilt: 52 Sayı: 2, 129 - 138, 01.04.2024
Öz
Kaynakça
- F. de Sa Alves, E. Barreiro, C. Manssour Fraga, From Nature to Drug Discovery: The Indole Scaffold as a “Privileged Structure,” Mini Rev. Med. Chem., 9 (2009) 782–793.
- P.F. Lamie, J.N. Philoppes, Design, synthesis, stereochemical determination, molecular docking study, in silico pre-ADMET prediction and anti-proliferative activities of indole-pyrimidine derivatives as Mcl-1 inhibitors, Bioorg. Chem., 116 (2021) 105335.
- H. Abdel-Gawad, H.A. Mohamed, K.M. Dawood, F.A.-R. Badria, Synthesis and Antiviral Activity of New Indole-Based Heterocycles, Chem. Pharm. Bull (Tokyo)., 58 (2010) 1529–1531.
- Y. Li, H. Wu, L. Tang, C. Feng, J. Yu, Y. Li, Y. Yang, B. Yang, Q. He, The potential insulin sensitizing and glucose lowering effects of a novel indole derivative in vitro and in vivo, Pharmacol. Res., 56 (2007) 335–343.
- M.S. Estevão, L.C. Carvalho, D. Ribeiro, D. Couto, M. Freitas, A. Gomes, L.M. Ferreira, E. Fernandes, M.M.B. Marques, Antioxidant activity of unexplored indole derivatives: Synthesis and screening, Eur. J. Med. Chem., 45 (2010) 4869–4878.
- S. Battaglia, E. Boldrini, F. Da Settimo, G. Dondio, C. La Motta, A.M. Marini, G. Primofiore, Indole amide derivatives: synthesis, structure–activity relationships and molecular modelling studies of a new series of histamine H1-receptor antagonists, Eur. J. Med. Chem., 34 (1999) 93–105.
- M.A.A. Radwan, E.A. Ragab, N.M. Sabry, S.M. El-Shenawy, Synthesis and biological evaluation of new 3-substituted indole derivatives as potential anti-inflammatory and analgesic agents, Bioorg. Med. Chem., 15 (2007) 3832–3841.
- A.Y. Alzahrani, Y.A. Ammar, M.A. Salem, M. Abu‐Elghait, A. Ragab, Design, synthesis, molecular modeling, and antimicrobial potential of novel 3‐[(1H ‐pyrazol‐3‐yl)imino]indolin‐2‐one derivatives as DNA gyrase inhibitors, Arch. Pharm (Weinheim)., 355 (2022) e2100266.
- S. Ghanei-Nasab, M. Khoobi, F. Hadizadeh, A. Marjani, A. Moradi, H. Nadri, S. Emami, A. Foroumadi, A. Shafiee, Synthesis and anticholinesterase activity of coumarin-3-carboxamides bearing tryptamine moiety, Eur. J. Med. Chem., 121 (2016) 40–46.
- S. Dadashpour, S. Emami, Indole in the target-based design of anticancer agents: A versatile scaffold with diverse mechanisms, Eur. J. Med. Chem., 150 (2018) 9–29.
- H. Sachdeva, J. Mathur, A. Guleria, Indole Derivatives as Potential Anticancer Agents: A Review, J. Chil. Chem. Soc., 65 (2020) 4900–4907.
- K. Kaur, V. Jaitak, Recent Development in Indole Derivatives as Anticancer Agents for Breast Cancer, Anticancer Agents Med. Chem., 19 (2019) 962–983.
- W. Cui, A. Aouidate, S. Wang, Q. Yu, Y. Li, and S. Yuan, Discovering Anti-Cancer Drugs via Computational Methods, Front Pharmacol., 11 (2020) 733.
- M. H. Baig, K. Ahmad, G. Rabbani, M. Danishuddin, and I. Choi, Computer Aided Drug Design and its Application to the Development of Potential Drugs for Neurodegenerative Disorders, Curr Neuropharmacol., 16 (2018) 740–748.
- H. M. Patel et al., “Design and synthesis of VEGFR-2 tyrosine kinase inhibitors as potential anticancer agents by virtual based screening,” RSC Adv, 5(2015) 56724–56771.
- R. Hanachi et al., “Structural, QSAR, machine learning and molecular docking studies of 5-thiophen-2-yl pyrazole derivatives as potent and selective cannabinoid-1 receptor antagonists,” New Journal of Chemistry, 45 (2021) 17796–17807.
- Ç. Karabacak, Ö. Dilek, Synthesis, solvatochromic properties and theoretical calculation of some novel disazo indole dyes, J. Mol. Liq., 199 (2014) 227–236.
- A. Daina, O. Michielin, V. Zoete, SwissTargetPrediction: updated data and new features for efficient prediction of protein targets of small molecules, Nucleic Acids Res., 47 (2019) W357–W364.
- 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., 31 (2010) 455–461.
- E.F. Pettersen, T.D. Goddard, C.C. Huang, G.S. Couch, D.M. Greenblatt, E.C. Meng, T.E. Ferrin, UCSF Chimera—A visualization system for exploratory research and analysis, J. Comput. Chem., 25 (2004) 1605–1612.
- BIOVIA (2021) Discovery Studio Visualizer, version 21.1.0.20298. Dassault Systèmes, San Diego, CA.
- B. Webb, A. Sali, Comparative Protein Structure Modeling Using MODELLER, Curr. Protoc. Bioinformatics, 54 (2016) 5.6.1-5.6.37.
- S. Russo, W.F. De Azevedo, Advances in the Understanding of the Cannabinoid Receptor 1 – Focusing on the Inverse Agonists Interactions, Curr. Med. Chem., 26 (2019) 1908–1919.
- Ç. Karabacak Atay, Ö. Dilek, T. Tilki, B. Dede, A novel imidazole-based azo molecule: synthesis, characterization, quantum chemical calculations, molecular docking, molecular dynamics simulations and ADMET properties, J. Mol. Model., 29 (2023) 226.
- M.D. Hanwell, D.E. Curtis, D.C. Lonie, T. Vandermeersch, E. Zurek, G.R. Hutchison, Avogadro: an advanced semantic chemical editor, visualization, and analysis platform, J. Cheminform., 4 (2012) 17.
- G. Xiong, Z. Wu, J. Yi, L. Fu, Z. Yang, C. Hsieh, M. Yin, X. Zeng, C. Wu, A. Lu, X. Chen, T. Hou, D. Cao, ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties, Nucleic Acids Res., 49 (2021) W5–W14.
- P. Banerjee, A.O. Eckert, A.K. Schrey, R. Preissner, ProTox-II: a webserver for the prediction of toxicity of chemicals, Nucleic Acids Res., 46 (2018) W257–W263.
- R. Hanachi, R. Ben Said, H. Allal, S. Rahali, M.A.M. Alkhalifah, F. Alresheedi, B. Tangour, M. Hochlaf, Structural, QSAR, machine learning and molecular docking studies of 5-thiophen-2-yl pyrazole derivatives as potent and selective cannabinoid-1 receptor antagonists, New J. Chem., 45 (2021) 17796–17807.
- G.S. Amato, A. Manke, D.L. Harris, R.W. Wiethe, V. Vasukuttan, R.W. Snyder, T.W. Lefever, R. Cortes, Y. Zhang, S. Wang, S.P. Runyon, R. Maitra, Blocking Alcoholic Steatosis in Mice with a Peripherally Restricted Purine Antagonist of the Type 1 Cannabinoid Receptor, J. Med. Chem., 61 (2018) 4370–4385.
Toplam 29 adet kaynakça vardır.
Ayrıntılar
| Birincil Dil | İngilizce |
|---|---|
| Konular | Biyomoleküler Modelleme ve Tasarım |
| Bölüm | Research Article |
| Yazarlar | |
| Yayımlanma Tarihi | 1 Nisan 2024 |
| Gönderilme Tarihi | 26 Ekim 2023 |
| Kabul Tarihi | 9 Aralık 2023 |
| Yayımlandığı Sayı | Yıl 2024 Cilt: 52 Sayı: 2 |
Kaynak Göster
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