How to cite this paper
Gowda, M., Vinay, B., Maitra, N., Kumaraswamy, S & Lokanath, N. (2023). Crystal structure, DFT, molecular docking and dynamics simulation studies of 4,4-dimethoxychalcone.Current Chemistry Letters, 12(3), 567-578.
Refrences
1. Sarda, S. R., Puri, V. A., Rode, A. B., Dalawe, T. N., Jadhav, W. N., & Pawar, R. P. (2007). Sulfated tin oxides: a suitable reagent for synthesis of 2, 4-diphenyl-4, 6, 7, 8-tetrahydrochromen-5-one. Arkivoc, 16, 246-251.
2. Hemingway, R. W. (1989). Structural variations in proanthocyanidins and their derivatives. In Chem and significance of condensed tannins (pp. 83-107). Springer, Boston, MA.
3. Harborne, J. B., Mabry, T. J. and Mabry, H. (1975). The Flavonoids Chapman and Hall. Biochemical systematics of flavonoids.
4. Pawlak, A., Henklewska, M., Hernández Suárez, B., Łużny, M., Kozłowska, E., Obmińska-Mrukowicz, B., & Janeczko, T. (2020). Chalcone methoxy derivatives exhibit antiproliferative and proapoptotic activity on canine lymphoma and leukemia cells. Molecules, 25(19), 4362.
5. Opletalova, V. (2000). Chalcones and their heterocyclic analogs as potential therapeutic agents in bacterial diseases. Ceska a Slovenska Farmacie: Casopis Ceske Farmaceuticke Spolecnosti a Slovenske Farmaceuticke Spolecnosti, 49(6), 278-284.
6. Konieczny, M. T., Konieczny, W., Sabisz, M., Skladanowski, A.,Wakiec, R., ́ Augustynowicz-Kopec, E. and Zwolska, Z. (2007). Synthesis of isomeric, oxathiolone fused chalcones, and comparisonof their activity toward various microorganisms and human cancercells line. Chem. Pharm. Bull., 55(5), 817-820.
7. Narender, T., Khaliq, T., Goyal, N., & Gupta, S. (2005). Synthesis of chromenochalcones and evaluation of their in vitro antileishmanial activity. Bioorg. Med. Chem., 13(23), 6543-6550.
8. Lee, S. H., Nan, J. X., Zhao, Y. Z., Woo, S. W., Park, E. J., Kang, T. H., ... & Sohn, D. H. (2003). The chalcone butein from Rhus verniciflua shows antifibrogenic activity. Planta Med., 69(11), 990-994.
9. Jin, F., Jin, X. Y., Jin, Y. L., Sohn, D. W., Kim, S. A., Sohn, D. H., ... & Kim, H. S. (2007). Structural requirements of 2′, 4′, 6′-tris (methoxymethoxy) chalcone derivatives for anti-inflammatory activity: The importance of a 2′-hydroxy moiety. Archives of pharmacal research, 30(11), 1359-1367.
10. Barfod, L., Kemp, K., Hansen, M., & Kharazmi, A. (2002). Chalcones from Chinese liquorice inhibit proliferation of T cells and production of cytokines. Int. Immunopharmacol., 2(4), 545-555.
11. Prasad, Y. R., Rao, A. L., & Rambabu, R. (2008). Synthesis and antimicrobial activity of some chalcone derivatives. J Chem, 5(3), 461-466.
12. Havranek, B., & Islam, S. M. (2021). An in silico approach for identification of novel inhibitors as potential therapeutics targeting COVID-19 main protease. Journal of Biomolecular Structure and Dynamics, 39(12), 4304-4315.
13. Bheenaveni, R. S. (2020). India’s indigenous idea of herd immunity: the solution for COVID-19?. Tradit. Med. Res., 5(4), 182.
14. Clarke, J. M., Majeed, A., & Beaney, T. (2021). Measuring the impact of covid-19. bmj, 373.
15. Fehr, A. R., & Perlman, S. (2015). Coronaviruses: an overview of their replication and pathogenesis. Coronaviruses, 1-23.
16. Ziebuhr, J., & Siddell, S. G. (1999). Processing of the human coronavirus 229E replicase polyproteins by the virus-encoded 3C-like proteinase: identification of proteolytic products and cleavage sites common to pp1a and pp1ab. Virol. J., 73(1), 177-185.
17. Thiel, V., Ivanov, K. A., Putics, A., Hertzig, T., Schelle, B., Bayer, S., & Ziebuhr, J. (2003). Mechanisms and enzymes involved in SARS coronavirus genome expression. J. Gen. Virol., 84(9), 2305-2315.
18. Snijder, E. J., Bredenbeek, P. J., Dobbe, J. C., Thiel, V., Ziebuhr, J., Poon, L. L., ... & Gorbalenya, A. E. (2003). Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage. J. Mol. Biol., 331(5), 991-1004.
19. Ziebuhr, J., Heusipp, G., & Siddell, S. G. (1997). Biosynthesis, purification, and characterization of the human coronavirus 229E 3C-like proteinase. Virol. J., 71(5), 3992-3997.
20. Hatada, R., Okuwaki, K., Mochizuki, Y., Handa, Y., Fukuzawa, K., Komeiji, Y., ... & Tanaka, S. (2020). Fragment molecular orbital based interaction analyses on COVID-19 main protease− inhibitor N3 complex (PDB ID: 6LU7). J Chem Inf Model, 60(7), 3593-3602.
21. Zhang, L., Lin, D., Sun, X., Curth, U., Drosten, C., Sauerhering, L., ... & Hilgenfeld, R. (2020). Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors. Science, 368(6489), 409-412.
22. Yang, S., Chen, S. J., Hsu, M. F., Wu, J. D., Tseng, C. T. K., Liu, Y. F., ... & Hsu, M. C. (2006). Synthesis, crystal structure, structure− activity relationships, and antiviral activity of a potent SARS coronavirus 3CL protease inhibitor. J. Med. Chem., 49(16), 4971-4980.
23. Chen, S., Hu, T., Zhang, J., Chen, J., Chen, K., Ding, J., ... & Shen, X. (2008). Mutation of Gly-11 on the dimer interface results in the complete crystallographic dimer dissociation of severe acute respiratory syndrome coronavirus 3C-like protease: crystal structure with molecular dynamics simulations. J. Biol. Chem., 283(1), 554-564.
24. Ravindra, H. J., Harrison, W. T. A., Kumar, M. S., & Dharmaprakash, S. M. (2009). Synthesis, crystal growth, characterization and structure–NLO property relationship in 1, 3-bis (4-methoxyphenyl) prop-2-en-1-one single crystal. Journal of crystal growth, 311(2), 310-315.
25. Expert, C. S. (2011). Rigaku Corporation. Tokyo, Japan.
26. Sheldrick, G. M. (2008). A short history of SHELX. Acta Crystallogr. A ACTA CRYSTALLOGR A, 64(1), 112-122.
27. Minor, W., Dauter, Z., Helliwell, J. R., Jaskolski, M., & Wlodawer, A. (2016). Safeguarding structural data repositories against bad apples. Structure, 24(2), 216-220.
28. Hema, M. K., Karthik, C. S., Pampa, K. J., Manukumar, H. M., Mallu, P., Warad, I., & Lokanath, N. K. (2019). Solvent induced 4, 4, 4-trifluoro-1-(2-naphthyl)-1, 3-butanedione Cu (II) complexes: Synthesis, structure, DFT calculation and biocidal activity. Polyhedron, 168, 127-137.
29. Spackman, P. R., Turner, M. J., McKinnon, J. J., Wolff, S. K., Grimwood, D. J., Jayatilaka, D., & Spackman, M. A. (2021). CrystalExplorer: A program for Hirshfeld surface analysis, visualization and quantitative analysis of molecular crystals. J. Appl. Crystallogr., 54(3), 1006-1011.
30. Pampa, K. J., Karthik, C. S., Hema, M. K., Mallu, P., & Lokanath, N. K. (2021). Post-synthetic modification of supramolecular assemblies of β-diketonato Cu (II) complexes: comparing and contrasting the molecular topology by crystal structure and quantum computational studies. Cryst. Eng. Comm., 23(24), 4344-4369.
31. Hema, M. K., Karthik, C. S., Pampa, K. J., Mallu, P., & Lokanath, N. K. (2020). Solvent induced mononuclear and dinuclear mixed ligand Cu (II) complex: structural diversity, supramolecular packing polymorphism and molecular docking studies. New J. Chem., 44(41), 18048-18068.
32. Frisch, M. E., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., ... & Fox, D. J. (2016). Gaussian 16.
33. Dewar, M. J., Holder, A. J., Dennington, R. D., Liotard, I. D. A., Truhlar, D. G., Keith, T. A., ... & Harris, C. D. (1994). AMPAC 8 User Manual.
34. Agrahari, A. K. (2017). A computational approach to identify a potential alternative drug with its positive impact toward PMP22. J. Cell. Biochem., 118(11), 3730-3743.
35. Trott, O., & Olson, A. J. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem., 31(2), 455-461.
36. Huey, R., Morris, G. M., & Forli, S. (2012). Using AutoDock 4 and AutoDock vina with AutoDockTools: a tutorial. The Scripps Research Institute Molecular Graphics Laboratory, 10550, 92037.
37. Studio, D. (2008). Discovery studio. Accelrys [2.1].
38. Mohamed, S. K., Mague, J. T., Akkurt, M., Alfayomy, A. M., Seri, S. M. A., Abdel-Raheem, S. A., & Ul-Malik, M. A. A. (2022). Crystal structure and Hirshfeld surface analysis of ethyl (3E)-5-(4-chlorophenyl)-3-{[(4-chlorophenyl) formamido] imino}-7-methyl-2H, 3H, 5H-[1, 3] thiazolo [3, 2-a] pyrimidine-6-carboxylate. Acta Crystallogr. E: Crystallogr. Commun., 78(8).
39. Kaid, M., Ali, A., Shamsan, A., Younes, S., Abdel-Raheem, S., Abdul-Malik, M & Salem, W. (2022). Efficiency of maturation oxidation ponds as a post-treatment technique of wastewater. Curr. Chem. Lett., 11(4), 415-422.
40. Fouad, M., Badawy, M., El-Aswad, A., & Aly, M. (2023). Experimental modeling design to study the effect of different soil treatments on the dissipation of metribuzin herbicide with effect on dehydrogenase activity. Curr. Chem. Lett., 12(2), 383-396.
41. Tolba, M., ul-Malik, M., El-Dean, A., Geies, A., Radwan, S., Zaki, R., Sayed, M., Mohamed, S & Abdel-Raheem, S. (2022). An overview on synthesis and reactions of coumarin based compounds. Curr. Chem. Lett., 11(1), 29-42.
42. Abd-Ella, A., Metwally, S., ul-Malik, M., El-Ossaily, Y., Elrazek, F., Aref, S., Naffea, Y & Abdel-Raheem, S. (2022). A review on recent advances for the synthesis of bioactive pyrazolinone and pyrazolidinedione derivatives. Curr. Chem. Lett., 11(2), 157-172.
43. Abdel-Raheem, S., El-Dean, A., Hassanien, R., El-Sayed, M., Abd-Ella, A., Zawam, S., & Tolba, M. (2022). Synthesis of new distyrylpyridine analogues bearing amide substructure as effective insecticidal agents. Curr. Chem. Lett., 11(1), 23-28.
2. Hemingway, R. W. (1989). Structural variations in proanthocyanidins and their derivatives. In Chem and significance of condensed tannins (pp. 83-107). Springer, Boston, MA.
3. Harborne, J. B., Mabry, T. J. and Mabry, H. (1975). The Flavonoids Chapman and Hall. Biochemical systematics of flavonoids.
4. Pawlak, A., Henklewska, M., Hernández Suárez, B., Łużny, M., Kozłowska, E., Obmińska-Mrukowicz, B., & Janeczko, T. (2020). Chalcone methoxy derivatives exhibit antiproliferative and proapoptotic activity on canine lymphoma and leukemia cells. Molecules, 25(19), 4362.
5. Opletalova, V. (2000). Chalcones and their heterocyclic analogs as potential therapeutic agents in bacterial diseases. Ceska a Slovenska Farmacie: Casopis Ceske Farmaceuticke Spolecnosti a Slovenske Farmaceuticke Spolecnosti, 49(6), 278-284.
6. Konieczny, M. T., Konieczny, W., Sabisz, M., Skladanowski, A.,Wakiec, R., ́ Augustynowicz-Kopec, E. and Zwolska, Z. (2007). Synthesis of isomeric, oxathiolone fused chalcones, and comparisonof their activity toward various microorganisms and human cancercells line. Chem. Pharm. Bull., 55(5), 817-820.
7. Narender, T., Khaliq, T., Goyal, N., & Gupta, S. (2005). Synthesis of chromenochalcones and evaluation of their in vitro antileishmanial activity. Bioorg. Med. Chem., 13(23), 6543-6550.
8. Lee, S. H., Nan, J. X., Zhao, Y. Z., Woo, S. W., Park, E. J., Kang, T. H., ... & Sohn, D. H. (2003). The chalcone butein from Rhus verniciflua shows antifibrogenic activity. Planta Med., 69(11), 990-994.
9. Jin, F., Jin, X. Y., Jin, Y. L., Sohn, D. W., Kim, S. A., Sohn, D. H., ... & Kim, H. S. (2007). Structural requirements of 2′, 4′, 6′-tris (methoxymethoxy) chalcone derivatives for anti-inflammatory activity: The importance of a 2′-hydroxy moiety. Archives of pharmacal research, 30(11), 1359-1367.
10. Barfod, L., Kemp, K., Hansen, M., & Kharazmi, A. (2002). Chalcones from Chinese liquorice inhibit proliferation of T cells and production of cytokines. Int. Immunopharmacol., 2(4), 545-555.
11. Prasad, Y. R., Rao, A. L., & Rambabu, R. (2008). Synthesis and antimicrobial activity of some chalcone derivatives. J Chem, 5(3), 461-466.
12. Havranek, B., & Islam, S. M. (2021). An in silico approach for identification of novel inhibitors as potential therapeutics targeting COVID-19 main protease. Journal of Biomolecular Structure and Dynamics, 39(12), 4304-4315.
13. Bheenaveni, R. S. (2020). India’s indigenous idea of herd immunity: the solution for COVID-19?. Tradit. Med. Res., 5(4), 182.
14. Clarke, J. M., Majeed, A., & Beaney, T. (2021). Measuring the impact of covid-19. bmj, 373.
15. Fehr, A. R., & Perlman, S. (2015). Coronaviruses: an overview of their replication and pathogenesis. Coronaviruses, 1-23.
16. Ziebuhr, J., & Siddell, S. G. (1999). Processing of the human coronavirus 229E replicase polyproteins by the virus-encoded 3C-like proteinase: identification of proteolytic products and cleavage sites common to pp1a and pp1ab. Virol. J., 73(1), 177-185.
17. Thiel, V., Ivanov, K. A., Putics, A., Hertzig, T., Schelle, B., Bayer, S., & Ziebuhr, J. (2003). Mechanisms and enzymes involved in SARS coronavirus genome expression. J. Gen. Virol., 84(9), 2305-2315.
18. Snijder, E. J., Bredenbeek, P. J., Dobbe, J. C., Thiel, V., Ziebuhr, J., Poon, L. L., ... & Gorbalenya, A. E. (2003). Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage. J. Mol. Biol., 331(5), 991-1004.
19. Ziebuhr, J., Heusipp, G., & Siddell, S. G. (1997). Biosynthesis, purification, and characterization of the human coronavirus 229E 3C-like proteinase. Virol. J., 71(5), 3992-3997.
20. Hatada, R., Okuwaki, K., Mochizuki, Y., Handa, Y., Fukuzawa, K., Komeiji, Y., ... & Tanaka, S. (2020). Fragment molecular orbital based interaction analyses on COVID-19 main protease− inhibitor N3 complex (PDB ID: 6LU7). J Chem Inf Model, 60(7), 3593-3602.
21. Zhang, L., Lin, D., Sun, X., Curth, U., Drosten, C., Sauerhering, L., ... & Hilgenfeld, R. (2020). Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors. Science, 368(6489), 409-412.
22. Yang, S., Chen, S. J., Hsu, M. F., Wu, J. D., Tseng, C. T. K., Liu, Y. F., ... & Hsu, M. C. (2006). Synthesis, crystal structure, structure− activity relationships, and antiviral activity of a potent SARS coronavirus 3CL protease inhibitor. J. Med. Chem., 49(16), 4971-4980.
23. Chen, S., Hu, T., Zhang, J., Chen, J., Chen, K., Ding, J., ... & Shen, X. (2008). Mutation of Gly-11 on the dimer interface results in the complete crystallographic dimer dissociation of severe acute respiratory syndrome coronavirus 3C-like protease: crystal structure with molecular dynamics simulations. J. Biol. Chem., 283(1), 554-564.
24. Ravindra, H. J., Harrison, W. T. A., Kumar, M. S., & Dharmaprakash, S. M. (2009). Synthesis, crystal growth, characterization and structure–NLO property relationship in 1, 3-bis (4-methoxyphenyl) prop-2-en-1-one single crystal. Journal of crystal growth, 311(2), 310-315.
25. Expert, C. S. (2011). Rigaku Corporation. Tokyo, Japan.
26. Sheldrick, G. M. (2008). A short history of SHELX. Acta Crystallogr. A ACTA CRYSTALLOGR A, 64(1), 112-122.
27. Minor, W., Dauter, Z., Helliwell, J. R., Jaskolski, M., & Wlodawer, A. (2016). Safeguarding structural data repositories against bad apples. Structure, 24(2), 216-220.
28. Hema, M. K., Karthik, C. S., Pampa, K. J., Manukumar, H. M., Mallu, P., Warad, I., & Lokanath, N. K. (2019). Solvent induced 4, 4, 4-trifluoro-1-(2-naphthyl)-1, 3-butanedione Cu (II) complexes: Synthesis, structure, DFT calculation and biocidal activity. Polyhedron, 168, 127-137.
29. Spackman, P. R., Turner, M. J., McKinnon, J. J., Wolff, S. K., Grimwood, D. J., Jayatilaka, D., & Spackman, M. A. (2021). CrystalExplorer: A program for Hirshfeld surface analysis, visualization and quantitative analysis of molecular crystals. J. Appl. Crystallogr., 54(3), 1006-1011.
30. Pampa, K. J., Karthik, C. S., Hema, M. K., Mallu, P., & Lokanath, N. K. (2021). Post-synthetic modification of supramolecular assemblies of β-diketonato Cu (II) complexes: comparing and contrasting the molecular topology by crystal structure and quantum computational studies. Cryst. Eng. Comm., 23(24), 4344-4369.
31. Hema, M. K., Karthik, C. S., Pampa, K. J., Mallu, P., & Lokanath, N. K. (2020). Solvent induced mononuclear and dinuclear mixed ligand Cu (II) complex: structural diversity, supramolecular packing polymorphism and molecular docking studies. New J. Chem., 44(41), 18048-18068.
32. Frisch, M. E., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., ... & Fox, D. J. (2016). Gaussian 16.
33. Dewar, M. J., Holder, A. J., Dennington, R. D., Liotard, I. D. A., Truhlar, D. G., Keith, T. A., ... & Harris, C. D. (1994). AMPAC 8 User Manual.
34. Agrahari, A. K. (2017). A computational approach to identify a potential alternative drug with its positive impact toward PMP22. J. Cell. Biochem., 118(11), 3730-3743.
35. Trott, O., & Olson, A. J. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem., 31(2), 455-461.
36. Huey, R., Morris, G. M., & Forli, S. (2012). Using AutoDock 4 and AutoDock vina with AutoDockTools: a tutorial. The Scripps Research Institute Molecular Graphics Laboratory, 10550, 92037.
37. Studio, D. (2008). Discovery studio. Accelrys [2.1].
38. Mohamed, S. K., Mague, J. T., Akkurt, M., Alfayomy, A. M., Seri, S. M. A., Abdel-Raheem, S. A., & Ul-Malik, M. A. A. (2022). Crystal structure and Hirshfeld surface analysis of ethyl (3E)-5-(4-chlorophenyl)-3-{[(4-chlorophenyl) formamido] imino}-7-methyl-2H, 3H, 5H-[1, 3] thiazolo [3, 2-a] pyrimidine-6-carboxylate. Acta Crystallogr. E: Crystallogr. Commun., 78(8).
39. Kaid, M., Ali, A., Shamsan, A., Younes, S., Abdel-Raheem, S., Abdul-Malik, M & Salem, W. (2022). Efficiency of maturation oxidation ponds as a post-treatment technique of wastewater. Curr. Chem. Lett., 11(4), 415-422.
40. Fouad, M., Badawy, M., El-Aswad, A., & Aly, M. (2023). Experimental modeling design to study the effect of different soil treatments on the dissipation of metribuzin herbicide with effect on dehydrogenase activity. Curr. Chem. Lett., 12(2), 383-396.
41. Tolba, M., ul-Malik, M., El-Dean, A., Geies, A., Radwan, S., Zaki, R., Sayed, M., Mohamed, S & Abdel-Raheem, S. (2022). An overview on synthesis and reactions of coumarin based compounds. Curr. Chem. Lett., 11(1), 29-42.
42. Abd-Ella, A., Metwally, S., ul-Malik, M., El-Ossaily, Y., Elrazek, F., Aref, S., Naffea, Y & Abdel-Raheem, S. (2022). A review on recent advances for the synthesis of bioactive pyrazolinone and pyrazolidinedione derivatives. Curr. Chem. Lett., 11(2), 157-172.
43. Abdel-Raheem, S., El-Dean, A., Hassanien, R., El-Sayed, M., Abd-Ella, A., Zawam, S., & Tolba, M. (2022). Synthesis of new distyrylpyridine analogues bearing amide substructure as effective insecticidal agents. Curr. Chem. Lett., 11(1), 23-28.