The synthesis, antimicrobial activity and docking studies of 6-(1H-benzimidazol-2-yl)-5-methylthieno[2,3-d]pyrimidin- 4(3H)-ones with acetamide and 1,2,4-oxadiazol-5-ylmethyl substituents




thiophene, pyrimidine, alkylation, antimicrobial agents, inhibitors, molecular docking


Aim. To synthesize, study the antimicrobial activity and suggest antimicrobial activity mechanism for the
novel derivatives of 6-(1H-benzimidazol-2-yl)-5-methylthieno[2,3-d]pyrimidin-4(3H)-one.
Results and discussion. As the result of the targeted modification of 6-(1H-benzimidazol-2-yl)-5-methylthieno[2,3-d]-pyrimidin-4(3H)-one in position 3 with acetamide and 1,2,4-oxadiazol-5-ylmethyl substituents, the compounds, which demonstrated better antimicrobial activity in the agar well diffusion assay than the reference drug Streptomycin, were obtained. To elucidate the mechanism of action of the novel compounds, the docking studies were con-
ducted to the active site of the 16S subunit of ribosomal RNA, the proven target for aminoglycoside antibiotics, as well as tRNA (Guanine37-N1)-methyltransferase (TrmD), which inhibitors were considered as a new potential class of antibiotics.
Experimental part. By the interaction of 6-(1H-benzimidazol-2-yl)-5-methylthieno[2,3-d]pyrimidin-4(3H)-one with a series of N-arylchloroacetamides and 3-aryl-5-(chloromethyl)-1,2,4-oxadiazoles in DMF in the presence of K2CO3 the target compounds were obtained. The antimicrobial activity was assessed by the agar well diffusion method. The concentration of microbial cells was determined by the McFarland standard; the value was 107 cells in 1 mL of the media. The 18 – 24 hour culture of microorganisms was used for tests. For the bacteria cultivation,
Müller-Hinton agar was used, Sabouraud agar was applied for C. albicans cultivation. The compounds were tested as the DMSO solution with the concentration of 100 µg/mL; the volume of the solution was 0.3 mL, the same volume was used for Streptomycin (the concentration 30 µg/mL). The docking studies were performed using Autodock Vina. Crystallographic data for the complexes of Streptomycin with the 16S subunit of ribosomal RNA
(1NTB) and its active site, as well as for tRNA (Guanine37-N1)-methyltransferase (EC; TrmD) (5ZHN) and its active site were obtained from the Protein Data Bank.
Conclusions. It has been determined that 2-[6-(1H-benzimidazol-2-yl)-5-methyl-4-oxothieno[2,3-d]pyrimidin-3(4H)-yl]-N-[4-(ethoxy)phenyl]acetamide, which is the most active as an antimicrobial agent among the compounds tested, also shows the best binding activity towards the active site of tRNA (guanine37-N1)-methyltransferase.

Supporting Agency

  • The research was funded by the Ministry of Health of Ukraine at the expense of the State Budget in the framework # 2301020 “Scientific and scientific-technical activity in the field of health protection” on the topic “Synthesis and study of new thienopyrimidines for detection of the antimicrobial and related types of pharmacological activity” (Order of the Ministry of Health of Ukraine of November 17, 2020 No. 2651).


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  1. Sherif, M. H.; Amr, A. E-G. E.; Assy, M. G.; Ramadan, Z. M. Synthesis of some new thienopyrimidine with benzoxazine, quinazoline and azole moieties. Afinidad 2008, 65 (535), 243 – 248.
  2. Tumkevicius, S.; Kaminskas, A.; Bucinskaite, V.; Labanauskas, L. Synthesis of 4,6-disubstituted thieno[2,3-d]pyrimidines from 4,6-dichloro-2-methylthiopyrimidine-5-carbaldehyde. Heterocycl. Commun. 2003, 9 (1), 89 – 94.
  3. Vlasov, S. V.; Kovalenko, S. M.; Chernykh, V. P.; Krolenko K. Yu. Synthesis and alkylation of 6-(1H-benzimidazol-2-yl)-5-methylthieno[2,3-d]pyrimidin-4(3H)-ones. Journal of Organic and Pharmaceutical Chemistry 2015, 13 (2), 30 – 34.
  4. Vlasov, S. V.; Kovalenko, S. N.; Osolodchenko, T. P.; Lenitskaya, E. B.; Chernykh, V. P. Synthesis and biological activity of 6-(1,3-benzoxazol-2-yl)-5-methylthieno-[2,3-d]pyrimidines. Pharm. Chem. J. 2018, 52 (6), 510 – 514.
  5. Aruna Kumari, M.; Triloknadh, S.; Harikrishna, N.; Vijjulatha, M.; Venkata Rao, C. Synthesis, Antibacterial Activity, and Docking Studies of 1,2,3-triazole-tagged Thieno[2,3-d]pyrimidinone Derivatives. J. Heterocycl. Chem. 2017, 54 (6), 3672-3681.
  6. Vlasov, S. V.; Zaremba, O. V.; Kovalenko, S. M.; Fedosov, A. I.; Chernykh, V. P. Synthesis of 5-methylthieno[2,3-d]pyrimidin-4(3H)-one derivatives modified in position 6 with 1,2,4- and 1,3,4-oxadiazoles and their biological activity. Journal of Organic and Pharmaceutical Chemistry 2011, 9 (4), 24 – 30.
  7. Vlasov, S. V.; Kovalenko, S. M.; Fedosov, A. I.; Chernykh, V. P. Synthesis of novel 3-substituted 1-alkyl-5-methyl-6-(3-aryl-1,2,4-oxadiazole-5-yl)thieno[2,3-d]pyrimidine-2,4(1H,3H)-diones and their antimicrobial activity. Journal of Organic and Pharmaceutical Chemistry 2011, 9 (3), 51 – 55.
  8. Vlasov, S. V.; Chernykh, V. P. Synthesis, antiinflammatory and antimicrobial activity of 6-(1H-benzimidazol-2-yl)-5-methyl-4-(alkylthio)thieno[2,3-d]pyrimidines. News of Pharmacy 2016, 3, 9 – 16.
  9. Vlasov, S. V.; Kovalenko, S. M.; Chernykh, V. P. Synthesis and the antimicrobial activity study of the novel derivatives of 4-oxo- and 4-thio-5-methyl-6-(1,2,4-oxadiazol-5-yl)thieno[2,3-d]pyrimidines. Journal of Chemical and Pharmaceutical Research 2015, 7 (4), 1043 – 1048.
  10. Ahmed, Z.; Saeed Khan, S.; Khan, M. In vitro trials of some antimicrobial combinations against Staphylococcus aureus and Pseudomonas aeruginosa. Saudi Journal of Biological Sciences 2013, 20 (1), 79 – 83.
  11. Araújo, S. G.; Alves, L. F.; Pinto, M. E. A.; Oliveira, G. T.; Siqueira, E. P.; Ribeiro, R. I. M. A.; Ferreira, J. M. S.; Lima, L. A. R. S. Volatile compounds of Lamiaceae exhibit a synergistic antibacterial activity with streptomycin. Braz. J. Microbiol. 2014, 45 (4), 1341 – 1347.
  12. Rodríguez-García, Á.; Mares-Alejandre, R. E.; Muñoz-Muñoz, P. L. A.; Ruvalcaba-Ruiz, S.; González-Sánchez, R. A.; Bernáldez-Sarabia, J.; Meléndez-López, S. G.; Licea-Navarro, A. F.; Ramos-Ibarra, M. A. Molecular Analysis of Streptomycin Resistance Genes in Clinical Strains of Mycobacterium tuberculosis and Biocomputational Analysis of the MtGidB L101F Variant. Antibiotics 2021, 10 (7), 807.
  13. Ward, H.; Perron, G. G.; Maclean, R. C. The cost of multiple drug resistance in Pseudomonas aeruginosa. Journal of Evolutionary Biology 2009, 22 (5), 997 – 1003.
  14. Jiang, L.; Patel, D. J. Solution structure of the tobramycin–RNA aptamer complex. Nature Structural Biology 1998, 5 (9), 769 – 774.
  15. Jiang, L.; Majumdar, A.; Hu, W.; Jaishree, T. J.; Xu, W.; Patel, D. J. Saccharide-RNA recognition in a complex formed between neomycin B and an RNA aptamer. Structure 1999, 7 (7), 817 – 827.
  16. Tereshko, V.; Skripkin, E.; Patel, D. J. Encapsulating Streptomycin within a Small 40-mer RNA. Chemistry & Biology 2003, 10 (2), 175 – 187.
  17. Zhong, W.; Pasunooti, K. K.; Balamkundu, S.; Wong, Y. H.; Nah, Q.; Gadi, V.; Gnanakalai, S.; Chionh, Y. H.; McBee, M. E.; Gopal, P.; Lim, S. H.; Olivier, N.; Buurman, E. T.; Dick, T.; Liu, C. F.; Lescar, J.; Dedon, P. C. Thienopyrimidinone Derivatives That Inhibit Bacterial tRNA (Guanine37-N1)-Methyltransferase (TrmD) by Restructuring the Active Site with a Tyrosine-Flipping Mechanism. J. Med. Chem. 2019, 62 (17), 7788 – 7805.
  18. Li, Y.; Zhong, W.; Koay, A. Z.; Ng, H. Q.; Koh-Stenta, X.; Nah, Q.; Lim, S. H.; Larsson, A.; Lescar, J.; Hill, J.; Dedon, P. C.; Kang, C. Backbone resonance assignment for the N-terminal region of bacterial tRNA-(N1G37) methyltransferase. Biomolecular NMR Assignments 2019, 13 (1), 49 – 53.
  19. Zhong, W.; Koay, A.; Ngo, A.; Li, Y.; Nah, Q.; Wong, Y. H.; Chionh, Y. H.; Ng, H. Q.; Koh-Stenta, X.; Poulsen, A.; Foo, K.; McBee, M.; Choong, M. L.; El Sahili, A.; Kang, C.; Matter, A.; Lescar, J.; Hill, J.; Dedon, P. Targeting the Bacterial Epitranscriptome for Antibiotic Development: Discovery of Novel tRNA-(N1G37) Methyltransferase (TrmD) Inhibitors. ACS Infectious Diseases 2019, 5 (3), 326 – 335.
  20. Jaroensuk, J; Wong, Y. H.; Zhong, W; Liew, C. W.; Maenpuen, S.; Sahili, A. E.; Atichartpongkul, S.; Chionh, Y. H.; Nah, Q.; Thongdee, N.; McBee, M. E.; Prestwich, E. G.; DeMott, M. S.; Chaiyen, P.; Mongkolsuk, S.; Dedon, P. C.; Lescar, J.; Fuangthong, M. Crystal structure and catalytic mechanism of the essential m1G37 tRNA methyltransferase TrmD from Pseudomonas aeruginosa. RNA 2019, 25 (11), 1481 – 1496.
  21. Pro zatverdzhennia metodychnykh vkazivok “Vyznachennia chutlyvosti mikroorhanizmiv do antybakterialnykh preparativ” [Methodological Instructions “Determination of the sensitivity of microorganisms to antibacterial drugs”]. (accessed June 11, 2021), Ministry of health of Ukraine, Order №167, 05.04.2007 (in Ukrainian).
  22. Bakteriolohichnyi kontrol pozhyvnykh seredovyshch [Bacteriological control of nutrient media]; Ministry of Health of Ukraine information letter No. 05.4.1/1670; Kyiv, 2001 (in Ukrainian).
  23. McFarland, J. The nephelometer: an instrument for estimating the number of bacteria in suspensions used for calculating the opsonic index and for vaccines. Journal of the American Medical Association 1907, XLIX (14), 1176 – 1178.
  24. Trott, O.; Olson, A. J. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem. 2010, 31 (2), 455 – 461.
  25. Tereshko, V.; Skripkin, E.; Patel, D. J. 2.9 Å crystal structure of Streptomycin RNA-aptamer complex. (accessed May 21, 2021),
  26. Zhong, W.; Pasunooti, K. K.; Balamkundu, S.; Wong, Y. W.; Nah, Q.; Liu, C. F.; Lescar, J.; Dedon, P. C. Crystal structure of TrmD from Pseudomonas aeruginosa in complex with active-site inhibitor. (accessed May 21, 2021),




How to Cite

Vlasov, S. V.; Borysov, O. V.; Severina, H. I.; Kovalenko, S. M.; Osolodchenko, T. P.; Vlasov, V. S.; Georgiyants, V. A. The Synthesis, Antimicrobial Activity and Docking Studies of 6-(1H-Benzimidazol-2-Yl)-5-methylthieno[2,3-d]pyrimidin- 4(3H)-Ones With Acetamide and 1,2,4-Oxadiazol-5-Ylmethyl Substituents. J. Org. Pharm. Chem. 2021, 19, 15-20.



Original Researches