From Chemistry Towards Technology Step-By-Step From Chemistry Towards Technology Step-By-Step От химии к технологии шаг за шагом 2782-1900 119505 10.52957/2782-1900-2026-7-1-164-172 Научные статьи Scientific articles Научные статьи In silico profiling of 3,4-dihydro-1H-[1,4]oxazino[4,3-a]benzimidazole derivatives: prediction of cytotoxic properties and ADME profile In silico profiling of 3,4-dihydro-1H-[1,4]oxazino[4,3-a]benzimidazole derivatives: prediction of cytotoxic properties and ADME profile Александрова Юлия Романовна Aleksandrova Yuliya Romanovna

кандидат биологических наук;

candidate of sciences in biology;

 Кучеренко Мария Викторовна Kucherenko Maria Viktorovna mariiaku1505@gmail.com Шагина Инна Александровна Shagina Inna Aleksandrovna Савина Луиза Ильинична Savina Luisa Ilyinichna luizasavina2000@mail.ru Бегунов Роман Сергеевич Begunov Roman Sergeevich begunov@bio.ac.ru

кандидат химических наук;

candidate of chemical sciences;

 Зубишина Алла Александровна Zubishina Alla Alexandrovna

кандидат биологических наук;

candidate of sciences in biology;

 Неганова Маргарита Евгеньевна Neganova Margarita Evgen'evna neganova83@mail.ru

доктор биологических наук;

doctor of sciences in biology;

 Ярославский государственный медицинский университет Yaroslavl State Medical University Институт элементоорганических соединений им. А.Н. Несмеянова РАН A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences Ярославский государственный университет им. П.Г. Демидова P.G. Demidov Yaroslavl State University 02 04 2026 02 04 2026 7 1 164 172 28 01 2026 05 03 2026 https://chemintech.ru/en/nauka/article/119505/view

Previously, we synthesised a series of 3,4-dihydro-1H-oxazino[4,3-a]benzimidazole derivatives by functionalising a benzimidazole derivative with an annulated morpholine ring in an SEAr reaction. Some compounds were not previously described in the literature. To assess their potential as pharmaceutical substances, the authors conducted an in silico analysis of the cytotoxic profile and pharmacokinetic parameters. Predicted cytotoxicity revealed a high probability of toxic effects on the nervous and respiratory systems for compounds with toxicity classes II to IV and LD50 in the range of 10-1500 mg/kg. The data obtained suggest a potential antitumour effect of the compounds against gliomas and lung cancer. Analysis of the ADME profile of the compounds showed that all molecules comply with Lipinski's rule. Therefore, further investigation of their antitumour potential in in vitro studies is prospective.

Previously, we synthesised a series of 3,4-dihydro-1H-oxazino[4,3-a]benzimidazole derivatives by functionalising a benzimidazole derivative with an annulated morpholine ring in an SEAr reaction. Some compounds were not previously described in the literature. To assess their potential as pharmaceutical substances, the authors conducted an in silico analysis of the cytotoxic profile and pharmacokinetic parameters. Predicted cytotoxicity revealed a high probability of toxic effects on the nervous and respiratory systems for compounds with toxicity classes II to IV and LD50 in the range of 10-1500 mg/kg. The data obtained suggest a potential antitumour effect of the compounds against gliomas and lung cancer. Analysis of the ADME profile of the compounds showed that all molecules comply with Lipinski's rule. Therefore, further investigation of their antitumour potential in in vitro studies is prospective.

 condensed benzimidazole derivatives morpholine ring prediction of cytotoxic profile pharmaceutical activity assessment of pharmacokinetic parameters The research was performed by Yaroslavl State Medical University, a federal state budgetary educational institution of higher education under the Ministry of Health of the Russian Federation as part of a state assignment for scientific research and development for 2025. The topic of the research is: ‘Development of new drugs for targeted chemotherapy of oncological diseases based on condensed benzimidazole derivatives with a nodal nitrogen atom.’

Ersan R.H., Kuzu B., Yetkin D., Alagoz M.A., Dogen A., Burmaoglu S. 2-Phenyl substituted Benzimidazole derivatives: Design, synthesis, and evaluation of their antiproliferative and antimicrobial activities. Med. Chem. Res, 2022, 16(31), 1192-1208. DOI: 10.1007/s00044-022-02900-3. Ersan R.H., Kuzu B., Yetkin D., Alagoz M.A., Dogen A., Burmaoglu S. 2-Phenyl substituted Benzimidazole derivatives: Design, synthesis, and evaluation of their antiproliferative and antimicrobial activities. Med. Chem. Res, 2022, 16(31), 1192-1208. DOI: 10.1007/s00044-022-02900-3. Pham E.C., Le Thi T.V., Ly Hong H.H., Vo Thi B.N., Vong L.B., Vu T.T., Vo D.D., Tran Nguyen N.V., Bao Le K.N., Truong T.N. N,2,6-Trisubstituted 1H-benzimidazole derivatives as a new scaffold of antimicrobial and anticancer agents: design, synthesis, in vitro evaluation, and in silico studies. RSC Adv., 2022, 13(1), 399-420. DOI:10.1039/d2ra06667j. Pham E.C., Le Thi T.V., Ly Hong H.H., Vo Thi B.N., Vong L.B., Vu T.T., Vo D.D., Tran Nguyen N.V., Bao Le K.N., Truong T.N. N,2,6-Trisubstituted 1H-benzimidazole derivatives as a new scaffold of antimicrobial and anticancer agents: design, synthesis, in vitro evaluation, and in silico studies. RSC Adv., 2022, 13(1), 399-420. DOI:10.1039/d2ra06667j. Bansal S., Gaur R., Bhardwaj H., Kumar N., Sharma G.K., Mishra S.S. Synthesis, biological evaluation, and molecular docking studies of benzimidazole derivatives substitutes as new antimicrobial agents. JDDMC, 2024, 10(2), 54-66. DOI: 10.11648/j.jddmc.20241002.12. Bansal S., Gaur R., Bhardwaj H., Kumar N., Sharma G.K., Mishra S.S. Synthesis, biological evaluation, and molecular docking studies of benzimidazole derivatives substitutes as new antimicrobial agents. JDDMC, 2024, 10(2), 54-66. DOI: 10.11648/j.jddmc.20241002.12. Ahmed A.E.R., Hassan Y.A.-E. Benzimidazole derivatives as potential chemotherapeutic agents. Curr. Drug Ther. 2013, 8(1), 1-14. DOI: 10.2174/1574885511308010001 Ahmed A.E.R., Hassan Y.A.-E. Benzimidazole derivatives as potential chemotherapeutic agents. Curr. Drug Ther. 2013, 8(1), 1-14. DOI: 10.2174/1574885511308010001 Akhtar W., Khan M.F., Verma G., Shaquiquzzaman M., Rizvi M.A., Mehdi S.H., Akhter M., Alam M.M. Therapeutic evolution of benzimidazole derivatives in the last quinquennial period. Eur. J. Med. Chem., 2017, 126, 705-753. DOI: /10.1016/j.ejmech.2016.12.010 Akhtar W., Khan M.F., Verma G., Shaquiquzzaman M., Rizvi M.A., Mehdi S.H., Akhter M., Alam M.M. Therapeutic evolution of benzimidazole derivatives in the last quinquennial period. Eur. J. Med. Chem., 2017, 126, 705-753. DOI: /10.1016/j.ejmech.2016.12.010 Begunov R.S., Egorov D.O., Chetvertakova A.V., Savina L.I., Zubishina A.A. Antibacterial activity of the halogenand nitro derivatives of benzimidazole against Bacillus Subtilis. Antibiot. Khimioter., 2023, 68(3-4), 19-24. DOI: 10.37489/0235-2990-2023-68-3-4-19-24. Begunov R.S., Egorov D.O., Chetvertakova A.V., Savina L.I., Zubishina A.A. Antibacterial activity of the halogenand nitro derivatives of benzimidazole against Bacillus Subtilis. Antibiot. Khimioter., 2023, 68(3-4), 19-24. DOI: 10.37489/0235-2990-2023-68-3-4-19-24. Begunov R.S., Zaitseva Y.V., Sokolov A.A., Egorov D.O., Filimonov S.I. Synthesis and Antibacterial Activity of 1,2,3,4-Tetrahydro- and Pyrido[1,2-a]benzimidazoles. Pharm. Chem. J., 2022, 56(1), 22–28. DOI: 10.1007/s11094-022-02596-0 Begunov R.S., Zaitseva Y.V., Sokolov A.A., Egorov D.O., Filimonov S.I. Synthesis and Antibacterial Activity of 1,2,3,4-Tetrahydro- and Pyrido[1,2-a]benzimidazoles. Pharm. Chem. J., 2022, 56(1), 22–28. DOI: 10.1007/s11094-022-02596-0 Nandwana N.K., Singh R.P., Patel O.P.S., Dhiman S., Saini H.K., Jha P.N., Kumar A. Design and Synthesis of Imidazo/Benzimidazo[1,2-c]quinazoline Derivatives and Evaluation of Their Antimicrobial Activity. ACS Omega, 2018, 3(11), 16338-16346. DOI: 10.1021/acsomega.8b01592. Nandwana N.K., Singh R.P., Patel O.P.S., Dhiman S., Saini H.K., Jha P.N., Kumar A. Design and Synthesis of Imidazo/Benzimidazo[1,2-c]quinazoline Derivatives and Evaluation of Their Antimicrobial Activity. ACS Omega, 2018, 3(11), 16338-16346. DOI: 10.1021/acsomega.8b01592. Mohamed B.G., Abdel-Alim A.M., Hussein M.A. Synthesis of 1-acyl-2-alkylthio-1,2,4-triazolobenzimidazoles with antifungal, anti-inflammatory and analgesic effects. Acta Pharm. 56(1 31-48. Mohamed B.G., Abdel-Alim A.M., Hussein M.A. Synthesis of 1-acyl-2-alkylthio-1,2,4-triazolobenzimidazoles with antifungal, anti-inflammatory and analgesic effects. Acta Pharm. 56(1 31-48. Huo X., Hou D., Wang H., He B., Fang J., Meng Y., Liu L., Wei Z., Wang Z., Liu F.W. Design, synthesis, in vitro and in vivo anti-respiratory syncytial virus (RSV) activity of novel oxizine fused benzimidazole derivatives. Eur. J. Med. Chem., 2021, 224, Article 113684. DOI: 10.1016/j.ejmech.2021.113684. Huo X., Hou D., Wang H., He B., Fang J., Meng Y., Liu L., Wei Z., Wang Z., Liu F.W. Design, synthesis, in vitro and in vivo anti-respiratory syncytial virus (RSV) activity of novel oxizine fused benzimidazole derivatives. Eur. J. Med. Chem., 2021, 224, Article 113684. DOI: 10.1016/j.ejmech.2021.113684. Wang H., Meng Y., Yang J., Huang H., Zhao Y., Zhu C., Wang C., Liu F.W. Design, synthesis and antitumour activity of novel 5(6)-amino-benzimidazolequinones containing a fused morpholine. Eur. J. Med. Chem., 2022, 238, Article 114420. DOI: 10.1016/j.ejmech.2022.114420. Wang H., Meng Y., Yang J., Huang H., Zhao Y., Zhu C., Wang C., Liu F.W. Design, synthesis and antitumour activity of novel 5(6)-amino-benzimidazolequinones containing a fused morpholine. Eur. J. Med. Chem., 2022, 238, Article 114420. DOI: 10.1016/j.ejmech.2022.114420. Aleksandrova Y., Savina L., Shagina I., Lyubina A., Zubishina A., Makarova S., Bagylly A., Khokhlov A., Begunov R., Neganova M. New Dihalogenated Derivatives of Condensed Benzimidazole Diones Promotes Cancer Cell Death Through Regulating STAT3/HK2 Axis/Pathway. Molecules, 2025, 30(21), 4150. DOI: 10.3390/molecules30214150 Aleksandrova Y., Savina L., Shagina I., Lyubina A., Zubishina A., Makarova S., Bagylly A., Khokhlov A., Begunov R., Neganova M. New Dihalogenated Derivatives of Condensed Benzimidazole Diones Promotes Cancer Cell Death Through Regulating STAT3/HK2 Axis/Pathway. Molecules, 2025, 30(21), 4150. DOI: 10.3390/molecules30214150 Begunov R.S., Aleksandrova Y.R., Shagina I.A., Kucherenko M.V., Pelyovin P.S., Khokhlov A.L., Neganova M.E. Cytotoxicity of a new condensed benzimidazoledione derivative against tumor and normal cell lines. Acta Biomedica Scientifica, 2025;10(6):12-19. (In Russ.) DOI: 10.29413/ABS.2025-10.6.2 Begunov R.S., Aleksandrova Y.R., Shagina I.A., Kucherenko M.V., Pelyovin P.S., Khokhlov A.L., Neganova M.E. Cytotoxicity of a new condensed benzimidazoledione derivative against tumor and normal cell lines. Acta Biomedica Scientifica, 2025;10(6):12-19. (In Russ.) DOI: 10.29413/ABS.2025-10.6.2 Sondhi S.M., Rajvanshi S., Johar M., Bharti N., Azam A., Singh A.K. Anti-inflammatory, analgesic and antiamoebic activity evaluation of pyrimido[1,6-a]benzimidazole derivatives synthesized by the reaction of ketoisothiocyanates with mono and diamines. Eur. J. Med. Chem., 2002, 37(10), 835-843. DOI:10.1016/s0223-5234(02)01403-4. Sondhi S.M., Rajvanshi S., Johar M., Bharti N., Azam A., Singh A.K. Anti-inflammatory, analgesic and antiamoebic activity evaluation of pyrimido[1,6-a]benzimidazole derivatives synthesized by the reaction of ketoisothiocyanates with mono and diamines. Eur. J. Med. Chem., 2002, 37(10), 835-843. DOI:10.1016/s0223-5234(02)01403-4. Sondhi S. M., Rani R., Singh J., Roy P., Agrawal S. K., Saxena A. K. Solvent free synthesis, anti-inflammatory and anticancer activity evaluation of tricyclic and tetracyclic benzimidazole derivatives. Bioorg. Med. Chem. Lett., 2010, 20(7), 2306-2310. DOI:10.1016/j.bmcl.2010.01.147. Sondhi S. M., Rani R., Singh J., Roy P., Agrawal S. K., Saxena A. K. Solvent free synthesis, anti-inflammatory and anticancer activity evaluation of tricyclic and tetracyclic benzimidazole derivatives. Bioorg. Med. Chem. Lett., 2010, 20(7), 2306-2310. DOI:10.1016/j.bmcl.2010.01.147. Begunov R.S., Savina L.I., Astafieva D.A. Intramolecular amination of ortho-nitro-tert-anilines as a method for the synthesis of condensed benzimidazole derivatives with a nodal nitrogen atom. From Chemistry Towards Technology Step-by-Step, 2025, 6(1), 88-98. DOI:10.52957/2782-1900-2025-6-1-88-98 Begunov R.S., Savina L.I., Astafieva D.A. Intramolecular amination of ortho-nitro-tert-anilines as a method for the synthesis of condensed benzimidazole derivatives with a nodal nitrogen atom. From Chemistry Towards Technology Step-by-Step, 2025, 6(1), 88-98. DOI:10.52957/2782-1900-2025-6-1-88-98 Kucherenko M.V., Savina L.I., Begunov R.S., Zubishina A.A., Gracheva E.L. Regioselectivity of the SEAr reaction of 8-chloro-3,4-dihydro-1H-[1,4]oxazino[4,3-a]benzimidazole. From Chemistry Towards Technology Step-by-Step, 2025, 6(4), 126-136. DOI: 10.52957/2782-1900-2025-6-4-126-136 Kucherenko M.V., Savina L.I., Begunov R.S., Zubishina A.A., Gracheva E.L. Regioselectivity of the SEAr reaction of 8-chloro-3,4-dihydro-1H-[1,4]oxazino[4,3-a]benzimidazole. From Chemistry Towards Technology Step-by-Step, 2025, 6(4), 126-136. DOI: 10.52957/2782-1900-2025-6-4-126-136 Balani S.K., Miwa G.T., Gan L.S., Wu J.T., Lee F.W. Strategy of utilizing in vitro and in vivo ADME tools for lead optimization and drug candidate selection. Curr Top Med Chem. 2005, 5(11), 1033-1038. DOI:10.2174/156802605774297038 Balani S.K., Miwa G.T., Gan L.S., Wu J.T., Lee F.W. Strategy of utilizing in vitro and in vivo ADME tools for lead optimization and drug candidate selection. Curr Top Med Chem. 2005, 5(11), 1033-1038. DOI:10.2174/156802605774297038 Daina A., Michielin O., Zoete V. SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci. Rep., 2017, 7, Article 42717. DOI: 10.1038/srep42717 Daina A., Michielin O., Zoete V. SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci. Rep., 2017, 7, Article 42717. DOI: 10.1038/srep42717 Manikandan P., Nagini S. Cytochrome P450 Structure, Function and Clinical Significance: A Review. Curr Drug Targets. 2018, 19(1), 38-54. DOI: 10.2174/1389450118666170125144557 Manikandan P., Nagini S. Cytochrome P450 Structure, Function and Clinical Significance: A Review. Curr Drug Targets. 2018, 19(1), 38-54. DOI: 10.2174/1389450118666170125144557 Banerjee P., Kemmler E., Dunkel M., Preissner R. ProTox 3.0: a webserver for the prediction of toxicity of chemicals. Nucleic Acids Res., 2024, 52(W1), W513-W520. DOI: 10.1093/nar/gkae303 Banerjee P., Kemmler E., Dunkel M., Preissner R. ProTox 3.0: a webserver for the prediction of toxicity of chemicals. Nucleic Acids Res., 2024, 52(W1), W513-W520. DOI: 10.1093/nar/gkae303