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AN UPDATE ON DOCKING ANALYSIS OF SOME PHARMACOLOGICAL ACTIVITY IN JAPANESE KNOTWEED LEAF COMPOUNDS

Year 2024, Volume: 8 Issue: 1, 54 - 61, 15.01.2024

Raja Kaliyaperumal Dr.tharını K

https://doi.org/10.33435/tcandtc.1173392

Abstract

The proof of concept presents the results of molecular docking analysis in common Japanese knotweed leaf compounds compared to the four different proteases 4GQQ, 2B17, 2FW3 and 1ZB6 obtained from the Protein Data Bank. Several of these compounds show binding energy for the various proteases and according to our data compare favorably to a known antibacterial, anti-inflammatory, anti diabetic and antioxidant drugs. The advancement of improved docking techniques has also made it possible to more accurately predict the biological activity of substances. This paper provides compounds of a Japanese knotweed plant leaf to determine the result of gas chromatography-mass spectrometry to calculate binding energy compared to standardized drugs. The lowest amount of binding energy for good biological activity. The compound undecane had a higher negative binding energy than 2-hydroxyethyl cyclohexanecarboxylate. As we can see from the docking results, by comparing the values of the binding energies of the four proteins obtained from the protein data bank (PDB) (4GQQ, 2B17, 2FW3 and 1ZB6) we propose that the undecane molecule better is antibacterial, anti-inflammatory anti diabetic and antioxidant nature then cyclohexane carboxylic acid 2-hydroxyethyl ester compound. The DFT results HOMO-LUMO energy difference value (E=-0.44eV) indicated that the compounds more stability and reactivity. So energy difference minimum value of 2-hydroxyethyl clohexane carboxylate has good chemical stability and reactivity nature compared to other compound.

Keywords

Japanese knotweed 4GQQ 2B17 2FW3 and HOMO-LUMO Japanese knotweed, 4GQQ, 2B17, 2FW3 and HOMO-LUMO

Supporting Institution

Government Arts college trichy, Tamil nadu

Project Number

nil

Thanks

Your early action in this regard is highly solicited. Thank you

References

  • [1] U.B. Bashtanova, K.P. Beckett, T.J. Flowers, Review: Physiological Approaches to the Improvement of Chemical Control of Japanese knotweed (Fallopia japonica), Weed Sci. (2009).
  • [2] K. Hari̇Smah, M. Mirzaei, K. Ghafari, Structural Analysis of Some Pyrrolopyrimidine Derivatives and Examining their Binding Affinity against Cyclooxygenase-2 Enzyme, Turk. Comput. Theor. Chem. (2021).
  • [3] T. Wunsch, M. Kelch, V. Röhl, H. Wieland, S. Labisch, M. van den Oever, T. Huber, J. Müssig, Structure-property relationships in Japanese knotweed – The potential of using the stem for composite applications, Ind. Crops Prod. 186 (2022) 115191.
  • [4] B. Colleran, S.N. Lacy, M.R. Retamal, Invasive Japanese knotweed ( Reynoutria japonica Houtt.) and related knotweeds as catalysts for streambank erosion, River Res. Appl. 36 (2020) 1962–1969.
  • [5] G. Sarkı, B. Tüzün, D. Ünlüer, H. Kantekin, Synthesis, characterization, chemical and biological activities of 4-(4-methoxyphenethyl)-5- benzyl-2-hydroxy-2H-1,2,4-triazole-3(4H)-one phthalocyanine derivatives, Inorganica Chim. Acta. 545 (2023) 121113.
  • [6] M.L. Hollingsworth, J.P. Bailey, Evidence for massive clonal growth in the invasive weed Fallopia japonica (Japanese knotweed), Bot. J. Linn. Soc. 133 (2000) 463–472.
  • [7] L.A. Weston, J.N. Barney, A. DiTommaso, A Review of the Biology and Ecology of Three Invasive Perennials in New York State: Japanese knotweed (Polygonum cuspidatum), Mugwort (Artemisia vulgaris) and Pale Swallow-wort (Vincetoxicum rossicum), Plant Soil. 277 (2005) 53–69.
  • [8] E. Delbart, G. Mahy, B. Weickmans, F. Henriet, S. Crémer, N. Pieret, S. Vanderhoeven, A. Monty, Can land managers control Japanese knotweed? Lessons from control tests in Belgium, Environ. Manage. 50 (2012) 1089–1097.
  • [9] J.L. Grimsby, R. Kesseli, Genetic composition of invasive Japanese knotweed s.l. in the United States, Biol. Invasions. 12 (2010) 1943–1946.
  • [10] Jones D, Fowler M S, Hocking S, Eastwood D Please don’t mow the Japanese knotweed NeoBiota 60 2020 19.
  • [11] M.S. Çelik, Ş.A. Çetinus, A.F. Yenidünya, S. Çetinkaya, B. Tüzün, Biosorption of Rhodamine B dye from aqueous solution by Rhus coriaria L. plant: Equilibrium, kinetic, thermodynamic and DFT calculations, J. Mol. Struct. 1272 (2023) 134158.
  • [12] A. Mermer, M. Volkan Bulbul, S. Mervenur Kalender, I. Keskin, B. Tuzun, O. Emre Eyupoglu, Benzotriazole-oxadiazole hybrid Compounds: Synthesis, anticancer Activity, molecular docking and ADME profiling studies, J. Mol. Liq. 359 (2022) 119264.
  • [13] O.A. Ladokun, A. Abiola, D. Okikiola, F. Ayodeji, GC-MS and molecular docking studies of Hunteria umbellata methanolic extract as a potent anti-diabetic, Inform. Med. Unlocked. 13 (2018) 1–8.
  • [14] B. Tüzün, Examination of anti-oxidant properties and molecular docking parameters of some compounds in human body, Turk. Comput. Theor. Chem. 4 (2020) 76–87.
  • [15] L. Hojatkashani̇, A.A. Omi̇di̇, Theoretical Methods for coding a strand of DNA bases and nucleotides with C2Fe+, A DFT study, Turk. Comput. Theor. Chem. 7 (2023) 20–33.
  • [16] Y. Eki̇nci̇oğlu, Theoretical analysis of ADP molecule in gas phase and aqueous solution: a DFT and PCM/TD-DFT study, Turk. Comput. Theor. Chem. 6 (2022) 31–41.
  • [17] A. Kaya, Theoretical studies of structural, optic and electronic properties of polypyrrole (PPy) oligomer, Turk. Comput. Theor. Chem. 2 (2018) 49–56.
  • [18] A. Kumer, M.N. Sarker, S. Paul, The thermo physical, HOMO, LUMO, Vibrational spectroscopy and QSAR study of morphonium formate and acetate Ionic Liquid Salts using computational method, Turk. Comput. Theor. Chem. 3 (2019) 59–68.

Year 2024, Volume: 8 Issue: 1, 54 - 61, 15.01.2024

Raja Kaliyaperumal Dr.tharını K

https://doi.org/10.33435/tcandtc.1173392

Abstract

Project Number

nil

References

  • [1] U.B. Bashtanova, K.P. Beckett, T.J. Flowers, Review: Physiological Approaches to the Improvement of Chemical Control of Japanese knotweed (Fallopia japonica), Weed Sci. (2009).
  • [2] K. Hari̇Smah, M. Mirzaei, K. Ghafari, Structural Analysis of Some Pyrrolopyrimidine Derivatives and Examining their Binding Affinity against Cyclooxygenase-2 Enzyme, Turk. Comput. Theor. Chem. (2021).
  • [3] T. Wunsch, M. Kelch, V. Röhl, H. Wieland, S. Labisch, M. van den Oever, T. Huber, J. Müssig, Structure-property relationships in Japanese knotweed – The potential of using the stem for composite applications, Ind. Crops Prod. 186 (2022) 115191.
  • [4] B. Colleran, S.N. Lacy, M.R. Retamal, Invasive Japanese knotweed ( Reynoutria japonica Houtt.) and related knotweeds as catalysts for streambank erosion, River Res. Appl. 36 (2020) 1962–1969.
  • [5] G. Sarkı, B. Tüzün, D. Ünlüer, H. Kantekin, Synthesis, characterization, chemical and biological activities of 4-(4-methoxyphenethyl)-5- benzyl-2-hydroxy-2H-1,2,4-triazole-3(4H)-one phthalocyanine derivatives, Inorganica Chim. Acta. 545 (2023) 121113.
  • [6] M.L. Hollingsworth, J.P. Bailey, Evidence for massive clonal growth in the invasive weed Fallopia japonica (Japanese knotweed), Bot. J. Linn. Soc. 133 (2000) 463–472.
  • [7] L.A. Weston, J.N. Barney, A. DiTommaso, A Review of the Biology and Ecology of Three Invasive Perennials in New York State: Japanese knotweed (Polygonum cuspidatum), Mugwort (Artemisia vulgaris) and Pale Swallow-wort (Vincetoxicum rossicum), Plant Soil. 277 (2005) 53–69.
  • [8] E. Delbart, G. Mahy, B. Weickmans, F. Henriet, S. Crémer, N. Pieret, S. Vanderhoeven, A. Monty, Can land managers control Japanese knotweed? Lessons from control tests in Belgium, Environ. Manage. 50 (2012) 1089–1097.
  • [9] J.L. Grimsby, R. Kesseli, Genetic composition of invasive Japanese knotweed s.l. in the United States, Biol. Invasions. 12 (2010) 1943–1946.
  • [10] Jones D, Fowler M S, Hocking S, Eastwood D Please don’t mow the Japanese knotweed NeoBiota 60 2020 19.
  • [11] M.S. Çelik, Ş.A. Çetinus, A.F. Yenidünya, S. Çetinkaya, B. Tüzün, Biosorption of Rhodamine B dye from aqueous solution by Rhus coriaria L. plant: Equilibrium, kinetic, thermodynamic and DFT calculations, J. Mol. Struct. 1272 (2023) 134158.
  • [12] A. Mermer, M. Volkan Bulbul, S. Mervenur Kalender, I. Keskin, B. Tuzun, O. Emre Eyupoglu, Benzotriazole-oxadiazole hybrid Compounds: Synthesis, anticancer Activity, molecular docking and ADME profiling studies, J. Mol. Liq. 359 (2022) 119264.
  • [13] O.A. Ladokun, A. Abiola, D. Okikiola, F. Ayodeji, GC-MS and molecular docking studies of Hunteria umbellata methanolic extract as a potent anti-diabetic, Inform. Med. Unlocked. 13 (2018) 1–8.
  • [14] B. Tüzün, Examination of anti-oxidant properties and molecular docking parameters of some compounds in human body, Turk. Comput. Theor. Chem. 4 (2020) 76–87.
  • [15] L. Hojatkashani̇, A.A. Omi̇di̇, Theoretical Methods for coding a strand of DNA bases and nucleotides with C2Fe+, A DFT study, Turk. Comput. Theor. Chem. 7 (2023) 20–33.
  • [16] Y. Eki̇nci̇oğlu, Theoretical analysis of ADP molecule in gas phase and aqueous solution: a DFT and PCM/TD-DFT study, Turk. Comput. Theor. Chem. 6 (2022) 31–41.
  • [17] A. Kaya, Theoretical studies of structural, optic and electronic properties of polypyrrole (PPy) oligomer, Turk. Comput. Theor. Chem. 2 (2018) 49–56.
  • [18] A. Kumer, M.N. Sarker, S. Paul, The thermo physical, HOMO, LUMO, Vibrational spectroscopy and QSAR study of morphonium formate and acetate Ionic Liquid Salts using computational method, Turk. Comput. Theor. Chem. 3 (2019) 59–68.
There are 18 citations in total.

Details

Primary Language English
Subjects Chemical Engineering
Journal Section Research Article
Authors

Raja Kaliyaperumal 0000-0002-2887-8398

Dr.tharını K 0000-0002-7705-6120

Project Number nil
Early Pub Date May 26, 2023
Publication Date January 15, 2024
Submission Date September 10, 2022
Published in Issue Year 2024 Volume: 8 Issue: 1

Cite

APA Kaliyaperumal, R., & K, D. (2024). AN UPDATE ON DOCKING ANALYSIS OF SOME PHARMACOLOGICAL ACTIVITY IN JAPANESE KNOTWEED LEAF COMPOUNDS. Turkish Computational and Theoretical Chemistry, 8(1), 54-61. https://doi.org/10.33435/tcandtc.1173392
AMA Kaliyaperumal R, K D. AN UPDATE ON DOCKING ANALYSIS OF SOME PHARMACOLOGICAL ACTIVITY IN JAPANESE KNOTWEED LEAF COMPOUNDS. Turkish Comp Theo Chem (TC&TC). January 2024;8(1):54-61. doi:10.33435/tcandtc.1173392
Chicago Kaliyaperumal, Raja, and Dr.tharını K. “AN UPDATE ON DOCKING ANALYSIS OF SOME PHARMACOLOGICAL ACTIVITY IN JAPANESE KNOTWEED LEAF COMPOUNDS”. Turkish Computational and Theoretical Chemistry 8, no. 1 (January 2024): 54-61. https://doi.org/10.33435/tcandtc.1173392.
EndNote Kaliyaperumal R, K D (January 1, 2024) AN UPDATE ON DOCKING ANALYSIS OF SOME PHARMACOLOGICAL ACTIVITY IN JAPANESE KNOTWEED LEAF COMPOUNDS. Turkish Computational and Theoretical Chemistry 8 1 54–61.
IEEE R. Kaliyaperumal and D. K, “AN UPDATE ON DOCKING ANALYSIS OF SOME PHARMACOLOGICAL ACTIVITY IN JAPANESE KNOTWEED LEAF COMPOUNDS”, Turkish Comp Theo Chem (TC&TC), vol. 8, no. 1, pp. 54–61, 2024, doi: 10.33435/tcandtc.1173392.
ISNAD Kaliyaperumal, Raja - K, Dr.tharını. “AN UPDATE ON DOCKING ANALYSIS OF SOME PHARMACOLOGICAL ACTIVITY IN JAPANESE KNOTWEED LEAF COMPOUNDS”. Turkish Computational and Theoretical Chemistry 8/1 (January 2024), 54-61. https://doi.org/10.33435/tcandtc.1173392.
JAMA Kaliyaperumal R, K D. AN UPDATE ON DOCKING ANALYSIS OF SOME PHARMACOLOGICAL ACTIVITY IN JAPANESE KNOTWEED LEAF COMPOUNDS. Turkish Comp Theo Chem (TC&TC). 2024;8:54–61.
MLA Kaliyaperumal, Raja and Dr.tharını K. “AN UPDATE ON DOCKING ANALYSIS OF SOME PHARMACOLOGICAL ACTIVITY IN JAPANESE KNOTWEED LEAF COMPOUNDS”. Turkish Computational and Theoretical Chemistry, vol. 8, no. 1, 2024, pp. 54-61, doi:10.33435/tcandtc.1173392.
Vancouver Kaliyaperumal R, K D. AN UPDATE ON DOCKING ANALYSIS OF SOME PHARMACOLOGICAL ACTIVITY IN JAPANESE KNOTWEED LEAF COMPOUNDS. Turkish Comp Theo Chem (TC&TC). 2024;8(1):54-61.

Journal Full Title: Turkish Computational and Theoretical Chemistry


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