Hirshfeld surface analysis, interaction energy calculations and in silico anti-SARS-CoV-2 potentials of metal (II) 3,4-dimethoxybenzoate with nicotinamide complexes
Abstract
In this study, types of the intermolecular interactions, the intermolecular interaction energies, void analysis of diaquabis(3,4-dimethoxybenzoate)bis(nicotinamide)zinc(II) dihydrate (Complex 1), diaquabis(3,4-dimethoxybenzoate)bis(nicotinamide)nickel(II) dihydrate (Complex 2), diaquabis(3,4-dimethoxybenzoate)bis(nicotinamide)cobalt(II) dihydrate (Complex 3), whose crystal structures were characterized before, were investigated with the help of the CrystalExplorer program (Version 21.5). It has been determined that H…H, H…O/O…H, H…C/C…H, H…N/N…H, C…C, C…O/O…C, O…O, and C…N/N…C interactions are intermolecular interactions that contribute to the Hirshfeld surface of the complexes. According to the results of the interaction energy analysis calculated with the help of B3LYP/6-31G(d,p), B3LYP/6-31G(d), B3LYP/3-21G, HF/6-31G(d,p), HF/6-31G(d), HF/3-21G, DFT/6-31G(d,p), DFT/6-31G(d), DFT/3-21G, MP2/6-31G(d,p), MP2/6-31G(d), MP2/3-21G basis sets, the major amount of the total energy is contributed by electrostatic and polarization energies. The interactions between Complexes 1-3 and the main protease enzyme and the spike protein of Omicron variant of the SARS-CoV-2 were investigated by Molecular docking studies. It was determined that complexes 1-3 and the main protease enzyme and the spike protein of Omicron variant of the SARS-CoV-2 interact via attractive charges, hydrogen bonding, electrostatic contacts, and hydrophobic interactions. According to the obtained results, further in vivo/in vitro studies are recommended for complex 3. The results determined as a result of interaction energy analysis and molecular docking studies show that the hydrogen bonds formed by the hydrogen bond donor/acceptor groups in the structure of the complexes are an important factor in both the stability of the crystal package and inhibition of important enzymes of SARS CoV-2.
Keywords
3 4-Dimethoxybenzoic acid transition metal complexes Hirshfeld surface analysis non-covalent interactions molecular docking SARS CoV-2.
Supporting Institution
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Project Number
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Thanks
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References
- Cramer, C.J., Essentials of computational chemistry: theories and models. Wiley, Chichester, West Sussex, England ; Hoboken, NJ, (2004).
- Jensen, F., Introduction to computational chemistry. John Wiley & Sons, Chichester, UK ; Hoboken, NJ, (2017).
- Lin, Z., Interplay between Theory and Experiment: Computational Organometallic and Transition Metal Chemistry. Accounts of Chemical Research, 43, 602–611, (2010). https://doi.org/10.1021/ar9002027
- Spackman, M.A., Jayatilaka, D., Hirshfeld surface analysis, CrystEngComm, 11, 19–32, (2009). https://doi.org/10.1039/B818330A
- Spackman, M.A., Spackman, P.R., Thomas, S.P., 13 Beyond Hirshfeld surface analysis: Interaction energies, energy frameworks and lattice energies with CrystalExplorer. In: 13 Beyond Hirshfeld surface analysis: Interaction energies, energy frameworks and lattice energies with CrystalExplorer. pp. 329–352. De Gruyter, (2021).
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- McKinnon, J.J., Fabbiani, F.P.A., Spackman, M.A., Comparison of Polymorphic Molecular Crystal Structures through Hirshfeld Surface Analysis, Crystal Growth & Design, 7, 755–769, (2007). https://doi.org/10.1021/cg060773k
- Vijesh, A.M., Isloor, A.M., Telkar, S., Arulmoli, T., Fun, H.-K., Molecular docking studies of some new imidazole derivatives for antimicrobial properties. Arabian Journal of Chemistry, 6, 197–204, (2013). https://doi.org/10.1016/j.arabjc.2011.10.007
- Shoichet, B.K., McGovern, S.L., Wei, B., Irwin, J.J., Lead discovery using molecular docking, Current Opinion in Chemical Biology, 6, 439–446, (2002). https://doi.org/10.1016/S1367-5931(02)00339-3
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- Daoud, S., Alabed, S.J., Dahabiyeh, L.A., Identification of potential COVID-19 main protease inhibitors using structure-based pharmacophore approach, molecular docking and repurposing studies, Acta Pharmaceutica. 71, 163–174 (2021). https://doi.org/10.2478/acph-2021-0016
- Kaya, A.A., Demircioğlu, Z., Kaya, E.Ç., Büyükgüngör, O., Synthesis, X-ray structural characterization, NLO, MEP, NBO and HOMO-LUMO analysis using DFT study of Zn(II)bis(3,4 dimethoxybenzoate)bis(nicotinamide) dihydrate, Heterocyclic Communications, 20, 51–59, (2014). https://doi.org/10.1515/hc-2013-0160
- Kaya, E.Ç., Kaya, A.A., Demircioğlu, Z., Büyükgüngör, O., Synthesis, spectroscopic characterization, X-ray structure and DFT calculations of Ni(II)bis(3,4 dimethoxybenzoate)bis(nicotinamide) dihydrate, Heterocyclic Communications, 23, 115–123, (2017). https://doi.org/10.1515/hc-2016-0099
- Kaya, A.A., Demircioğlu, Z., Kaya, E.Ç., Büyükgüngör, O., Synthesis, X-ray structural characterization, NLO, MEP, NBO and HOMO-LUMO analysis using DFT study of Zn(II)bis(3,4 dimethoxybenzoate)bis(nicotinamide) dihydrate, Heterocyclic Communications, 20, 51–59, (2014). https://doi.org/10.1515/hc-2013-0160
- Spackman, M.A., Jayatilaka, D., Hirshfeld surface analysis, CrystEngComm, 11, 19–32, (2009). https://doi.org/10.1039/B818330A
- Hirshfeld, F.L.: Bonded-atom fragments for describing molecular charge densities. Theoret. Chim. Acta. 44, 129–138 (1977). https://doi.org/10.1007/BF00549096
- Spackman, M.A., Jayatilaka, D., Hirshfeld surface analysis, CrystEngComm, 11, 19–32, (2009). https://doi.org/10.1039/B818330A
- Spackman, P.R., Turner, M.J., McKinnon, J.J., Wolff, S.K., Grimwood, D.J., Jayatilaka, D., Spackman, M.A., CrystalExplorer : a program for Hirshfeld surface analysis, visualization and quantitative analysis of molecular crystals, Journal of Applied Crystallography, 54, 1006–1011, (2021). https://doi.org/10.1107/S1600576721002910
- McKinnon, J.J., Jayatilaka, D., Spackman, M.A., Towards quantitative analysis of intermolecular interactions with Hirshfeld surfaces, Chemical Communications, 3814–3816, (2007). https://doi.org/10.1039/b704980c
- Trott, O., Olson, A.J., AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading, Journal of Computational Chemistry, 31, 455, (2009). https://doi.org/10.1002/jcc.21334
- Fakhar, Z., Khan, S., AlOmar, S.Y., Alkhuriji, A., Ahmad, A., ABBV-744 as a potential inhibitor of SARS-CoV-2 main protease enzyme against COVID-19, Scientific Reports, 11, 234, (2021). https://doi.org/10.1038/s41598-020-79918-3
- Bank, R.P.D., RCSB PDB - 7T9J: Cryo-EM structure of the SARS-CoV-2 Omicron spike protein, https://www.rcsb.org/structure/7T9J
- BIOVIA, Dassault Systèmes, BIOVA Discovery Studio Visualizer 2021, v21.1.0.20298, San Diego: Dassault Systèmes, (2021).
Metal (II) 3,4-dimetoksibenzoatın nikotinamid komplekslerinin Hirshfeld yüzey analizi, etkileşim enerjisi hesaplamaları ve in silico anti-SARS-CoV-2 potansiyelleri
Abstract
Bu çalışmada, kristal yapıları daha önce karakterize edilmiş olan metal (II) 3,4-dimetoksibenzoatın nikotinamid komplekslerinin moleküllerarası etkileşim türleri, moleküllerarası etkileşim enerjileri ve boşluk analizi CrystalExplorer programı (Versiyon 21.5) yardımıyla incelenmiştir. H…H, H…O/O…H, H…C/C…H, H…N/N…H, C…C, C…O/O…C, O…O ve C…N/N…C etkileşimleri, komplekslerin Hirshfeld yüzeyine katkıda bulunan moleküller arası etkileşimlerdir. Hesaplanan etkileşim enerjisi analizi sonuçlarına göre, toplam enerjiye en önemli katkıyı elektrostatik ve polarizasyon enerjileri sağlamaktadır. Çalışmada ayrıca, kompleks 1-3 ile SARS CoV-2'nin ana proteaz enzimi ve Omicron varyantının spike proteini arasındaki etkileşimler Moleküler docking çalışmaları ile incelenmiştir. Kompleks 1-3'ün, yükler arası çekim kuvvetleri, hidrojen bağı, elektrostatik ve hidrofobik etkileşimler yoluyla SARS-CoV-2'nin ana proteaz enzimi ve Omicron varyantının spike proteini ile etkileşime girdiği belirlenmiştir. Elde edilen sonuçlara göre özellikle kompleks 3 için ileri in vivo/in vitro çalışmalar önerilmektedir. Etkileşim enerjisi analizi ve moleküler docking çalışmaları sonucunda belirlenen sonuçlar komplekslerin yapısında bulunan hidrojen bağı donor akseptor gruplar vasıtasıyla oluşan hidrojen bağlarının gerek kristal paketin kararlılığına gerekse SARS CoV-2'nin önemli enzimlerini inhibe etmede önemli birer faktör olduğunu göstermektedir.
Keywords
3 4-Dimetoksibenzoik asit geçiş metal kompleksleri Hirshfeld yüzey analizi kovalent olmayan etkileşimler moleküler docking SARS CoV-2.
Project Number
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References
- Cramer, C.J., Essentials of computational chemistry: theories and models. Wiley, Chichester, West Sussex, England ; Hoboken, NJ, (2004).
- Jensen, F., Introduction to computational chemistry. John Wiley & Sons, Chichester, UK ; Hoboken, NJ, (2017).
- Lin, Z., Interplay between Theory and Experiment: Computational Organometallic and Transition Metal Chemistry. Accounts of Chemical Research, 43, 602–611, (2010). https://doi.org/10.1021/ar9002027
- Spackman, M.A., Jayatilaka, D., Hirshfeld surface analysis, CrystEngComm, 11, 19–32, (2009). https://doi.org/10.1039/B818330A
- Spackman, M.A., Spackman, P.R., Thomas, S.P., 13 Beyond Hirshfeld surface analysis: Interaction energies, energy frameworks and lattice energies with CrystalExplorer. In: 13 Beyond Hirshfeld surface analysis: Interaction energies, energy frameworks and lattice energies with CrystalExplorer. pp. 329–352. De Gruyter, (2021).
- McKinnon, J.J., Jayatilaka, D., Spackman, M.A., Towards quantitative analysis of intermolecular interactions with Hirshfeld surfaces, Chemical Communications, 3814, (2007). https://doi.org/10.1039/b704980c
- McKinnon, J.J., Fabbiani, F.P.A., Spackman, M.A., Comparison of Polymorphic Molecular Crystal Structures through Hirshfeld Surface Analysis, Crystal Growth & Design, 7, 755–769, (2007). https://doi.org/10.1021/cg060773k
- Vijesh, A.M., Isloor, A.M., Telkar, S., Arulmoli, T., Fun, H.-K., Molecular docking studies of some new imidazole derivatives for antimicrobial properties. Arabian Journal of Chemistry, 6, 197–204, (2013). https://doi.org/10.1016/j.arabjc.2011.10.007
- Shoichet, B.K., McGovern, S.L., Wei, B., Irwin, J.J., Lead discovery using molecular docking, Current Opinion in Chemical Biology, 6, 439–446, (2002). https://doi.org/10.1016/S1367-5931(02)00339-3
- Jain, S., Potschka, H., Chandra, P.P., Tripathi, M., Vohora, D., Management of COVID-19 in patients with seizures: Mechanisms of action of potential COVID-19 drug treatments and consideration for potential drug-drug interactions with anti-seizure medications, Epilepsy Research, 174, 106675, (2021). https://doi.org/10.1016/j.eplepsyres.2021.106675
- Cheke, R.S., The Molecular Docking Study of Potential Drug Candidates Showing Anti-COVID-19 Activity by Exploring of Therapeutic Targets of SARS-CoV-2, The Eurasian Journal of Medicine and Oncology (EJMO), (2020). https://doi.org/10.14744/ejmo.2020.31503
- Singh, S., Florez, H., Coronavirus disease 2019 drug discovery through molecular docking, F1000Research, 9, 502, (2020). https://doi.org/10.12688/f1000research.24218.1
- Parmar, G., Shah, A., Shah, S., Seth, A.K., Identification of bioactive phytoconstituents from the plant euphorbia hirta as potential inhibitor of sars-cov-2: An in-silico approach, Biointerface Research in Applied Chemistry, 1385–1396, (2022).
- Daoud, S., Alabed, S.J., Dahabiyeh, L.A., Identification of potential COVID-19 main protease inhibitors using structure-based pharmacophore approach, molecular docking and repurposing studies, Acta Pharmaceutica. 71, 163–174 (2021). https://doi.org/10.2478/acph-2021-0016
- Kaya, A.A., Demircioğlu, Z., Kaya, E.Ç., Büyükgüngör, O., Synthesis, X-ray structural characterization, NLO, MEP, NBO and HOMO-LUMO analysis using DFT study of Zn(II)bis(3,4 dimethoxybenzoate)bis(nicotinamide) dihydrate, Heterocyclic Communications, 20, 51–59, (2014). https://doi.org/10.1515/hc-2013-0160
- Kaya, E.Ç., Kaya, A.A., Demircioğlu, Z., Büyükgüngör, O., Synthesis, spectroscopic characterization, X-ray structure and DFT calculations of Ni(II)bis(3,4 dimethoxybenzoate)bis(nicotinamide) dihydrate, Heterocyclic Communications, 23, 115–123, (2017). https://doi.org/10.1515/hc-2016-0099
- Kaya, A.A., Demircioğlu, Z., Kaya, E.Ç., Büyükgüngör, O., Synthesis, X-ray structural characterization, NLO, MEP, NBO and HOMO-LUMO analysis using DFT study of Zn(II)bis(3,4 dimethoxybenzoate)bis(nicotinamide) dihydrate, Heterocyclic Communications, 20, 51–59, (2014). https://doi.org/10.1515/hc-2013-0160
- Spackman, M.A., Jayatilaka, D., Hirshfeld surface analysis, CrystEngComm, 11, 19–32, (2009). https://doi.org/10.1039/B818330A
- Hirshfeld, F.L.: Bonded-atom fragments for describing molecular charge densities. Theoret. Chim. Acta. 44, 129–138 (1977). https://doi.org/10.1007/BF00549096
- Spackman, M.A., Jayatilaka, D., Hirshfeld surface analysis, CrystEngComm, 11, 19–32, (2009). https://doi.org/10.1039/B818330A
- Spackman, P.R., Turner, M.J., McKinnon, J.J., Wolff, S.K., Grimwood, D.J., Jayatilaka, D., Spackman, M.A., CrystalExplorer : a program for Hirshfeld surface analysis, visualization and quantitative analysis of molecular crystals, Journal of Applied Crystallography, 54, 1006–1011, (2021). https://doi.org/10.1107/S1600576721002910
- McKinnon, J.J., Jayatilaka, D., Spackman, M.A., Towards quantitative analysis of intermolecular interactions with Hirshfeld surfaces, Chemical Communications, 3814–3816, (2007). https://doi.org/10.1039/b704980c
- Trott, O., Olson, A.J., AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading, Journal of Computational Chemistry, 31, 455, (2009). https://doi.org/10.1002/jcc.21334
- Fakhar, Z., Khan, S., AlOmar, S.Y., Alkhuriji, A., Ahmad, A., ABBV-744 as a potential inhibitor of SARS-CoV-2 main protease enzyme against COVID-19, Scientific Reports, 11, 234, (2021). https://doi.org/10.1038/s41598-020-79918-3
- Bank, R.P.D., RCSB PDB - 7T9J: Cryo-EM structure of the SARS-CoV-2 Omicron spike protein, https://www.rcsb.org/structure/7T9J
- BIOVIA, Dassault Systèmes, BIOVA Discovery Studio Visualizer 2021, v21.1.0.20298, San Diego: Dassault Systèmes, (2021).
Details
| Primary Language | English |
|---|---|
| Subjects | Macromolecular and Materials Chemistry (Other) |
| Journal Section | Research Articles |
| Authors | |
| Project Number | - |
| Early Pub Date | July 6, 2023 |
| Publication Date | July 7, 2023 |
| Submission Date | November 12, 2022 |
| Published in Issue | Year 2023 Volume: 25 Issue: 2 |