Startseite Naturwissenschaften Binding interaction of benzamide derivatives as inhibitors of DNA gyrase and Sec14p using Molegro Virtual Docker based on binding free energy
Artikel
Lizenziert
Nicht lizenziert Erfordert eine Authentifizierung

Binding interaction of benzamide derivatives as inhibitors of DNA gyrase and Sec14p using Molegro Virtual Docker based on binding free energy

  • Anaum Ihsan EMAIL logo , Rasheed Ahmad Khera EMAIL logo , Javed Iqbal und Muhammad Asgher
Veröffentlicht/Copyright: 21. Januar 2022
Zeitschrift für Physikalische Chemie
Aus der Zeitschrift Zeitschrift für Physikalische Chemie Band 236 Heft 4

Abstract

The docking simulation of benzamide derivatives as ligands and protein targets (DNA–gyrase) was performed and Sec14p binding mode interaction was predicted based on binding free energy analysis. Software Molegro Virtual Docking (MVD) was used to visualize the ligand–protein binding interactions. The results indicated the prevalence of steric or hydrophobic interactions among all the benzamide ligands besides hydrogen bonding or electrostatic interactions. The compounds B2, B4 against DNA gyrase, and compounds B3, B5 against Sec14p showed an uncompetitive pattern of inhibition as compared with the reference molecule. While compounds B1, B5 exhibited the best MolDock scores, i.e., −109.736 and −114.391 kcal/mol respectively for DNA gyrase, also compounds B1 and B2 against Sec14p displayed −100.105 and −119.451 kcal/mol sequentially. It was evident from the comparison of MolDock score for both the bacterial and fungal protein receptors that all the ligands were found to be more potent against DNA gyrase than Sec14p. However, only compound B2 with MolDock score −119.451 kcal/mol showed exceptional activity against Sec14p and was predicted to have potency as a lead compound to find a new anti-fungal therapeutic agent. Docking studies further highlighted the unique interactions such as tail-end hydrophobic rings of benzamide inhibitors with catalytically important amino acid residues, allowing flexibility in binding to both the receptors different from other inhibitors. These findings showed us that B1, B2 against Staphylococcus aureus and B5 against Saccharomyces cerevisiae could be leading compounds to discover new multidrug-resistant strains.

Keywords: benzamide derivatives; binding energy; ligand; molecular docking; molegro virtual docker; receptor
Corresponding authors: Anaum Ihsan and Rasheed Ahmad Khera, Department of Chemistry, University of Agriculture, Faisalabad, 38000, Pakistan, E-mail: (A. Ihsan), (R.A. Khera)

Acknowledgments

We are thankful to Dr. Muhammad Khalid, for the computational resources for docking studies, Assistant Professor, Department of Chemistry, Khwaja Fareed University of Engineering & Information Technology, 64200-Rahim Yar Khan, Pakistan.

  1. Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Research funding: None declared.

  3. Conflict of interest statement: The authors declare no conflicts of interest regarding this article.

References

1. Tahir, M. B., Farman, S., Rasheed, A., Alrobei, H., Shahzad, K., Ali, A. M., Muhammad, S. Z. Phys. Chem. 2022, 236, 169–180, https://doi.org/10.1515/zpch-2021-3060.Suche in Google Scholar

2. Kasraei, R., Malakootian, M., Mohamadi, M. Z. Phys. Chem. 2021, 235, 885–908.Suche in Google Scholar

3. Tijar, R., Bourjila, M., Guerdaoui, A. E., El Merbouh, B., El Bouzaidi, R. D., El Gridani, A. Chem. Int. 2017, 3, 477–486.Suche in Google Scholar

4. Bourjila, M., El Gridani, A., Tijar, R., El Merbouh, B., Drissi, R., Bouzaidi, E. Chem. Int. 2018, 4, 216–220.Suche in Google Scholar

5. Habib, A., Bhatti, H. N., Iqbal, M., Asim, S., Mansha, A. Z. Phys. Chem. 2019, 233, 1645–1657; https://doi.org/10.1515/zpch-2018-1340.Suche in Google Scholar

6. Frombach, J., Lohan, S. B., Lemm, D., Gruner, P., Hasler, J., Ahlberg, S., Blume-Peytavi, U., Unbehauen, M., Haag, R., Meinke, M. C., Vogt, A. 2018. 232, 919–933; https://doi.org/10.1515/zpch-2017-1048.Suche in Google Scholar

7. Nisar, J., Iqbal, M., Iqbal, M., Shah, A., Akhter, M. S., Khan, R. A., Uddin, I., Shah, L. A., Khan, M. S. Z. Phys. Chem. 2020, 234, 117–128; https://doi.org/10.1515/zpch-2018-1273.Suche in Google Scholar

8. Kamran, U., Bhatti, H. N., Iqbal, M., Nazir, A. Z. Phys. Chem. 2019, 233, 1325–1349; https://doi.org/10.1515/zpch-2018-1238.Suche in Google Scholar

9. Lomesh, S. K., Nathan, V., Bala, M., Kumar, I. Z. Phys. Chem. 2020, 234, 1853–1874; https://doi.org/10.1515/zpch-2019-1386.Suche in Google Scholar

10. Shehatta, I. Z. Phys. Chem. 2001, 215, 605.10.1524/zpch.2001.215.5.605Suche in Google Scholar

11. Bourjila, M., El Gridani, A., Tijar, R., El Merbouh, B., Drissi, R., Bouzaidi, E. Chem. Int. 2019, 5, 132–142.Suche in Google Scholar

12. Tijar, R., El Merbouh, B., Bourjila, M., Guerdaoui, A., El Bouzaidi, R. D., El Gridani, A., Mouhtadi, M. Chem. Int. 2016, 2, 201–221.Suche in Google Scholar

13. Ukpaka, C. P. Chem. Int. 2019, 5, 143–157.Suche in Google Scholar

14. Nikodimos, Y., Hagos, B., Dereje, D., Hussen, M. Chem. Int. 2018, 4, 43–51.Suche in Google Scholar

15. Tijar, R., Bourjila, M., Guerdaoui, A., El Merbouh, B., El Bouzaidi, R. D., El Gridani, A. Chem. Int. 2017, 3, 477–486.Suche in Google Scholar

16. Sun, C.-Y., Li, Y.-S., Shi, A.-L., Li, Y.-F., Cao, R.-F., Ding, H.-W., Yin, Q.-Q., Zhang, L.-J., Zheng, H.-C., Song, H.-R. Chin. Chem. Lett. 2015, 26, 1307–1310; https://doi.org/10.1016/j.cclet.2015.06.017.Suche in Google Scholar

17. Wang, X.-M., Xu, J., Xin, M.-H., Lu, S.-M., Zhang, S.-Q. Bioorg. Med. Chem. Lett 2015, 25, 1730–1735; https://doi.org/10.1016/j.bmcl.2015.02.067.Suche in Google Scholar PubMed

18. Sakr, A., Kothayer, H., Ibrahim, S. M., Baraka, M. M., Rezq, S. Bioorg. Chem. 2019, 84, 76–86; https://doi.org/10.1016/j.bioorg.2018.11.030.Suche in Google Scholar PubMed

19. Czaplewski, L. G., Collins, I., Boyd, E. A., Brown, D., East, S. P., Gardiner, M., Fletcher, R., Haydon, D. J., Henstock, V., Ingram, P. Bioorg. Med. Chem. Lett 2009, 19, 524–527; https://doi.org/10.1016/j.bmcl.2008.11.021.Suche in Google Scholar PubMed

20. Bala, S., Sharma, N., Kajal, A., Kamboj, S. Sci. World J. 2014, 2014, 1–9; https://doi.org/10.1155/2014/732141.Suche in Google Scholar PubMed PubMed Central

21. Kim, B. J., Kim, J., Kim, Y.-K., Choi, S.-Y., Choo, H.-Y. P. Bull. Kor. Chem. Soc. 2010, 31, 1270–1274; https://doi.org/10.5012/bkcs.2010.31.5.1270.Suche in Google Scholar

22. Jiang, Z., Wang, H., Li, Y., Peng, Z., Li, Y., Li, Z. Acta Pharm. Sin. B 2015, 5, 201–209; https://doi.org/10.1016/j.apsb.2015.03.013.Suche in Google Scholar PubMed PubMed Central

23. Mitachi, K., Salinas, Y. G., Connelly, M., Jensen, N., Ling, T., Rivas, F. Bioorg. Med. Chem. Lett 2012, 22, 4536–4539; https://doi.org/10.1016/j.bmcl.2012.05.124.Suche in Google Scholar PubMed

24. Ören, İ. Y., Şener, E. A., Ertaş, C., Arpaci, Ö. T., Yalçin, İ., Altanlar, N. Turk. J. Chem. 2004, 28, 441–450.Suche in Google Scholar

25. Ertan, T., Yildiz, I., Ozkan, S., Temiz-Arpaci, O., Kaynak, F., Yalcin, I., Aki-Sener, E., Abbasoglu, U. Bioorg. Med. Chem. 2007, 15, 2032–2044; https://doi.org/10.1016/j.bmc.2006.12.035.Suche in Google Scholar PubMed

26. Acar, C., Yalçın, G., Ertan-Bolelli, T., Onurdağ, F. K., Ökten, S., Şener, F., Yıldız, İ. Bioorg. Chem. 2020, 94, 103368; https://doi.org/10.1016/j.bioorg.2019.103368.Suche in Google Scholar PubMed

27. Nagaraj, K., Arunachalam, S. Z. Phys. Chem. 2013, 227, 1687–1706; https://doi.org/10.1524/zpch.2013.0374.Suche in Google Scholar

28. Morgner, N., Barth, H. D., Schmidt, T. L., Heckel, A., Scheffer, U., Göbel, M., Fucini, P., Brutschy, B. Z. Phys. Chem. 2007, 221, 689–704; https://doi.org/10.1524/zpch.2007.221.5.689.Suche in Google Scholar

29. Suzuki, R., Nozawa, D., Futamura, A., Nishikawa-Shimono, R., Abe, M., Hattori, N., Ohta, H., Araki, Y., Kambe, D., Ohmichi, M. Bioorg. Med. Chem. 2015, 23, 1260–1275; https://doi.org/10.1016/j.bmc.2015.01.044.Suche in Google Scholar PubMed

30. Łażewska, D., Kieć-Kononowicz, K. Expert Opin. Ther. Pat. 2014, 24, 89–111.10.1517/13543776.2014.848197Suche in Google Scholar PubMed

31. Djeha, A. H., Thomson, T. A., Leung, H., Searle, P. F., Young, L. S., Kerr, D. J., Harris, P. A., Mountain, A., Wrighton, C. J. Mol. Ther. 2001, 3, 233–240; https://doi.org/10.1006/mthe.2000.0250.Suche in Google Scholar PubMed

32. Gorlewska, K., Mazerska, Z., Sowiński, P., Konopa, J. Chem. Res. Toxicol. 2001, 14, 1–10; https://doi.org/10.1021/tx000081c.Suche in Google Scholar PubMed

33. Çelik, A., Yetiş, G. Bioorg. Med. Chem. 2012, 20, 3540–3550.10.1016/j.bmc.2012.04.004Suche in Google Scholar PubMed

34. Rajamuthiah, R., Fuchs, B. B., Conery, A. L., Kim, W., Jayamani, E., Kwon, B., Ausubel, F. M., Mylonakis, E. PLoS One 2015, 10, e0124595; https://doi.org/10.1371/journal.pone.0124595.Suche in Google Scholar PubMed PubMed Central

35. Karthik, L., Kumar, G., Keswani, T., Bhattacharyya, A., Chandar, S. S., Rao, K. B. PLoS One 2014, 9, e90972; https://doi.org/10.1371/journal.pone.0090972.Suche in Google Scholar PubMed PubMed Central

36. Mrozik, H., Jones, H., Friedman, J., Schwartzkopf, G., Schardt, R., Patchett, A., Hoff, D., Yakstis, J., Riek, R., Ostlind, D. Experientia 1969, 25, 883; https://doi.org/10.1007/bf01897937.Suche in Google Scholar PubMed

37. Cuena, B. R., Maciá, M. M. Atención Primaria 1998, 21, 289.Suche in Google Scholar

38. Waszkowycz, B., Clark, D. E., Gancia, E. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2011, 1, 229–259; https://doi.org/10.1002/wcms.18.Suche in Google Scholar

39. Yuriev, E., Ramsland, P. A. J. Mol. Recogn. 2013, 26, 215–239; https://doi.org/10.1002/jmr.2266.Suche in Google Scholar PubMed

40. Pagadala, N. S., Syed, K., Tuszynski, J. Biophys. Rev. 2017, 9, 91–102; https://doi.org/10.1007/s12551-016-0247-1.Suche in Google Scholar PubMed PubMed Central

41. Rohs, R., Bloch, I., Sklenar, H., Shakked, Z. Nucleic Acids Res. 2005, 33, 7048–7057; https://doi.org/10.1093/nar/gki1008.Suche in Google Scholar PubMed PubMed Central

42. Guedes, I. A., de Magalhães, C. S., Dardenne, L. E. Biophys. Rev. 2014, 6, 75–87; https://doi.org/10.1007/s12551-013-0130-2.Suche in Google Scholar

43. Chou, K.-C. Curr. Med. Chem. 2004, 11, 2105–2134; https://doi.org/10.2174/0929867043364667.Suche in Google Scholar

44. Reindl, W., Yuan, J., Krämer, A., Strebhardt, K., Berg, T. J. Chem. Biol. 2008, 15, 459–466; https://doi.org/10.1016/j.chembiol.2008.03.013.Suche in Google Scholar

45. Schneider, G., Böhm, H.-J. Drug Discov. Today 2002, 7, 64–70; https://doi.org/10.1016/s1359-6446(02)00004-1.Suche in Google Scholar

46. Naeem, S., Hylands, P., Barlow, D. J. Appl. Pharmaceut. Sci. 2013, 3, 13.Suche in Google Scholar

47. Durdagi, S., ul Qamar, M. T., Salmas, R. E., Tariq, Q., Anwar, F., Ashfaq, U. A. J. Mol. Graph. Model. 2018, 85, 122–129; https://doi.org/10.1016/j.jmgm.2018.07.010.Suche in Google Scholar PubMed

48. Nile, A. H., Tripathi, A., Yuan, P., Mousley, C. J., Suresh, S., Wallace, I. M., Shah, S. D., Pohlhaus, D. T., Temple, B., Nislow, C., Giaever, G. Nat. Chem. Biol. 2014, 10, 76–84; https://doi.org/10.1038/nchembio.1389.Suche in Google Scholar PubMed PubMed Central

49. D. Studio and I. Insight: San Diego, CA, 2009; p. 92121.Suche in Google Scholar

50. Kusumaningrum, S., Budianto, E., Kosela, S., Sumaryono, W., Juniarti, F. J. Appl. Pharmaceut. Sci. 2014, 4, 047–053.Suche in Google Scholar

51. Drlica, K., Zhao, X. Microbiol. Mol. Biol. Rev. 1997, 61, 377–392; https://doi.org/10.1128/mmbr.61.3.377-392.1997.Suche in Google Scholar PubMed PubMed Central

52. Tsuzuki, S., Honda, K., Uchimaru, T., Mikami, M., Tanabe, K. J. Am. Chem. Soc. 2002, 124, 104–112; https://doi.org/10.1021/ja0105212.Suche in Google Scholar PubMed

53. Meyer, E. A., Castellano, R. K., Diederich, F. Angewandte Chem. Int. Edit. 2003, 42, 1210–1250. https://doi.org/10.1002/anie.200390319.Suche in Google Scholar PubMed

54. Clark, T., Hennemann, M., Murray, J. S., Politzer, P. J. Mol. Model. 2007, 13, 291–296; https://doi.org/10.1007/s00894-006-0130-2.Suche in Google Scholar PubMed

55. Politzer, P., Murray, J. S., Clark, T. Phys. Chem. Chem. Phys. 2013, 15, 11178–11189; https://doi.org/10.1039/c3cp00054k.Suche in Google Scholar PubMed

56. de Freitas, R. F., Schapira, M. Medchemcomm 2017, 8, 1970–1981; https://doi.org/10.1039/c7md00381a.Suche in Google Scholar PubMed PubMed Central

57. Pries, V., Nöcker, C., Khan, D., Johnen, P., Hong, Z., Tripathi, A., Keller, A.-L., Fitz, M., Perruccio, F., Filipuzzi, I. Cell Chem. Biol. 2018, 25, 279–290. e277; https://doi.org/10.1016/j.chembiol.2017.12.007.Suche in Google Scholar PubMed PubMed Central

58. Filipuzzi, I., Cotesta, S., Perruccio, F., Knapp, B., Fu, Y., Studer, C., Pries, V., Riedl, R., Helliwell, S. B., Petrovic, K. T. J. PLoS Genetics 2016, 12, e1006374; https://doi.org/10.1371/journal.pgen.1006374.Suche in Google Scholar PubMed PubMed Central

59. Olsen, L., Pettersson, I., Hemmingsen, L., Adolph, H.-W., Jørgensen, F. S. J. J. Comput. Aided Mol. Des. 2004, 18, 287–302; https://doi.org/10.1023/b:jcam.0000046821.15502.71.10.1023/B:JCAM.0000046821.15502.71Suche in Google Scholar

60. Subramanian, A., Jaganathan, S., Manikandan, A., Pandiaraj, K., Gomathi, N., Supriyanto, E. RSC Adv. 2016, 6, 48294–48314; https://doi.org/10.1039/c6ra07802h.Suche in Google Scholar

61. Suhail, M., Ali, I. Chem. Int. 2020, 6, 277–294.Suche in Google Scholar

62. Patel, R., Kumar, S., Verma, A., Srivastava, S. Chem. Int. 2017, 3, 158–164.Suche in Google Scholar

63. Aljameel, S., Almessiere, M. A., Khan, F. A., Taskhandi, N., Slimani, Y., Al-Saleh, N. S., Manikandan, A., Al-Suhaimi, E. A., Baykal, A. Nanomaterials 2021, 11, 700; https://doi.org/10.3390/nano11030700.Suche in Google Scholar PubMed PubMed Central

64. Algarou, N. A., Slimani, Y., Almessiere, M. A., Sadaqat, A., Trukhanov, A. V., Gondal, M. A., Hakeem, A. S., Trukhanov, S. V., Vakhitov, M. G., Klygach, D. S. Nanomaterials 2020, 10, 2134; https://doi.org/10.3390/nano10112134.Suche in Google Scholar PubMed PubMed Central

65. Pradhan, A., Vishwakarma, S. Chem. Int. 2020, 6, 224–231.Suche in Google Scholar

66. Vellayappan, M., Jaganathan, S., Manikandan, A. RSC Adv. 2016, 6, 114859–114878; https://doi.org/10.1039/c6ra24590k.Suche in Google Scholar

67. Jaganathan, S. K., Mani, M. P., Nageswaran, G., Krishnasamy, N. P., Manikandan, A. Polym. Test. 2018, 70, 244–254; https://doi.org/10.1016/j.polymertesting.2018.07.015.Suche in Google Scholar

68. Manikandan, A., Mani, M. P., Jaganathan, S. K., Rajasekar, R. Polym. Compos. 2018, 39, E132–E139; https://doi.org/10.1002/pc.24463.Suche in Google Scholar

69. Jaganathan, S. K., Mani, M. P., Khudzari, A. Z. M., Ismail, A. F., Manikandan, A., Rathanasamy, R. Int. J. Polym. Anal. Char. 2019, 24, 696–708; https://doi.org/10.1080/1023666x.2019.1662590.Suche in Google Scholar

70. Jaganathan, S. K., Mani, M. P., Manikandan, A., Rathanasamy, R. Polym. Test. 2019, 78, 105955; https://doi.org/10.1016/j.polymertesting.2019.105955.Suche in Google Scholar

71. Jaganathan, S. K., Mani, M. P., Nageswaran, G., Krishnasamy, N. P., Manikandan, A. Int. J. Polym. Anal. Char. 2019, 24, 204–218; https://doi.org/10.1080/1023666x.2018.1564127.Suche in Google Scholar

72. Sasmaz, A., Ozkan, S., Gursu, M. F., Sasmaz, M. Appl. Radiat. Isot. 2017, 129, 185–188; https://doi.org/10.1016/j.apradiso.2017.07.060.Suche in Google Scholar PubMed

Received: 2021-08-28
Accepted: 2022-01-05
Published Online: 2022-01-21
Published in Print: 2022-04-26

© 2022 Walter de Gruyter GmbH, Berlin/Boston

Artikel in diesem Heft

  1. Frontmatter
  2. Review Article
  3. X-ray photoemission studies of the interaction of metals and metal ions with DNA
  4. Original Papers
  5. Back to the roots: the concepts of force and energy
  6. Synthesis and inhibitive characteristic of two acryloyl chloride derivatives towards the corrosion of API 5L X52 carbon steel in hydrochloric acid medium
  7. Binding interaction of benzamide derivatives as inhibitors of DNA gyrase and Sec14p using Molegro Virtual Docker based on binding free energy
  8. Kinetics of acid blue 40 dye degradation under solar light in the presence of CuO nanoparticles synthesized using Citrullus lanatus seeds extract
https://doi.org/10.1515/zpch-2021-3119
Schlagwörter für diesen Artikel
benzamide derivatives; binding energy; ligand; molecular docking; molegro virtual docker; receptor

Artikel in diesem Heft

  1. Frontmatter
  2. Review Article
  3. X-ray photoemission studies of the interaction of metals and metal ions with DNA
  4. Original Papers
  5. Back to the roots: the concepts of force and energy
  6. Synthesis and inhibitive characteristic of two acryloyl chloride derivatives towards the corrosion of API 5L X52 carbon steel in hydrochloric acid medium
  7. Binding interaction of benzamide derivatives as inhibitors of DNA gyrase and Sec14p using Molegro Virtual Docker based on binding free energy
  8. Kinetics of acid blue 40 dye degradation under solar light in the presence of CuO nanoparticles synthesized using Citrullus lanatus seeds extract
Jetzt anmelden und 20% sparen
Institutioneller Zugang
Wie funktioniert Authentifizierung?
Haben Sie eine Idee, wie wir unsere Website verbessern können?
Bitte schreiben Sie uns.
© 2025 De Gruyter Brill
Heruntergeladen am 8.12.2025 von https://www.degruyterbrill.com/document/doi/10.1515/zpch-2021-3119/pdf
Button zum nach oben scrollen