Synthesis, biological profile and computational insights of new derivatives of benzo [B][1,4] diazepines as prospective anticancer agents for inhibiting the CDK-2 protein

References

• A., Amin, Z.-U., Khazir, A., Ji, B., Bhat, D., Murtaza, A. A., Hurrah, I. A., Bhat, S., Parveen, S., Nisar., & P. K., Sharma. (2023). Anti-lung cancer activity of synthesized substituted 1, 4-benzothiazines: An insight from molecular docking and experimental studies. Anti-Cancer Agents in Medicinal Chemistry, 23, 1-14. https://doi.org/10.2174/0118715206276737231103114924
   Google Scholar
• Abd El-Karim, S. S., Syam, Y. M., El Kerdawy, A. M., & Abdelghany, T. M. (2019). New thiazol-hydrazono-coumarin hybrids targeting human cervical cancer cells: Synthesis, CDK2 inhibition, QSAR and molecular docking studies. Bioorganic Chemistry, 86, 80–96. https://doi.org/10.1016/j.bioorg.2019.01.026
   PubMed Web of Science ®Google Scholar
• Adam, R. W., Al-Labban, H. M., Kadhim, IN., & Aljanaby, A. A. J. (2019). Synthesis, characterization, and antibacterial activity of some new pyrimidine derivatives from chalcone derivatives. Drug Invention Today, 11(7), 1732–1739.
   Google Scholar
• Aihara, J-I. (1999). Reduced HOMO − LUMO gap as an index of kinetic stability for polycyclic aromatic hydrocarbons. Journal of Physical Chemistry A, 103(37), 7487–7495. https://doi.org/10.1021/jp990092i
   Web of Science ®Google Scholar
• Al Sheikh Ali, A., Khan, D., Naqvi, A., Al-Blewi, F. F., Rezki, N., Aouad, M. R., & Hagar, M. (2020). Design, synthesis, molecular modeling, anticancer studies, and density functional theory calculations of 4-(1, 2, 4-triazol-3-ylsulfanylmethyl)-1, 2, 3-triazole derivatives. ACS Omega, 6(1), 301–316. https://doi.org/10.1021/acsomega.0c04595
   PubMed Web of Science ®Google Scholar
• Anil, S. M., Shobith, R., Kiran, K. R., Swaroop, T. R., Mallesha, N., & Sadashiva, M. P. (2019). Facile synthesis of 1, 4-benzodiazepine-2, 5-diones and quinazolinones from amino acids as anti-tubercular agents. New Journal of Chemistry, 43(1), 182–187. https://doi.org/10.1039/C8NJ04936J
   Web of Science ®Google Scholar
• Asghar, U., Witkiewicz, A. K., Turner, N. C., & Knudsen, E. S. (2015). The history and future of targeting cyclin-dependent kinases in cancer therapy. Nature Reviews. Drug Discovery, 14(2), 130–146. https://doi.org/10.1038/nrd4504
   PubMed Web of Science ®Google Scholar
• Aversa, M. C., Ferlazzo, A., Giannetto, P., & Kohnke, F. H. (1986). A convenient synthesis of novel [1, 2, 4] triazolo [4, 3-a][1, 5] benzodiazepine derivatives, Synthesis. Synthesis, 1986(03), 230–231. https://doi.org/10.1055/s-1986-31628
   Google Scholar
• Besson, A., Dowdy, S. F., & Roberts, J. M. (2008). CDK inhibitors: Cell cycle regulators and beyond. Developmental Cell, 14(2), 159–169. https://doi.org/10.1016/j.devcel.2008.01.013
   PubMed Web of Science ®Google Scholar
• Bowers, K. J., Chow, E., Xu, H., Dror, R. O., Eastwood, M. P., Gregersen, B. A., Klepeis, J. L., Kolossvary, I., Moraes, M. A., & Sacerdoti, F. D. (2006). Scalable algorithms for molecular dynamics simulations on commodity clusters. In Proceedings of the 2006 ACM/IEEE Conference on Supercomputing (pp. 84-es)
   Google Scholar
• Cai, D., Byth, K. F., & Shapiro, G. I. (2006). AZ703, an imidazo [1, 2-a] pyridine inhibitor of cyclin-dependent kinases 1 and 2, induces E2F-1-dependent apoptosis enhanced by depletion of cyclin-dependent kinase 9. Cancer Research, 66(1), 435–444. https://doi.org/10.1158/0008-5472.CAN-05-1769
   PubMed Web of Science ®Google Scholar
• Chandrashekar, D. S., Karthikeyan, S. K., Korla, P. K., Patel, H., Shovon, A. R., Athar, M., Netto, G. J., Qin, Z. S., Kumar, S., Manne, U., Creighton, C. J., & Varambally, S. (2022). UALCAN: An update to the integrated cancer data analysis platform. Neoplasia (New York, N.Y.), 25, 18–27. https://doi.org/10.1016/j.neo.2022.01.001
   PubMed Web of Science ®Google Scholar
• Cheng, W., Yang, Z., Wang, S., Li, Y., Wei, H., Tian, X., & Kan, Q. (2019). Recent development of CDK inhibitors: An overview of CDK/inhibitor co-crystal structures. European Journal of Medicinal Chemistry, 164, 615–639. https://doi.org/10.1016/j.ejmech.2019.01.003
   PubMed Web of Science ®Google Scholar
• Chin, C.-H., Chen, S.-H., Wu, H.-H., Ho, C.-W., Ko, M.-T., & Lin, C.-Y. (2014). cytoHubba: Identifying hub objects and sub-networks from complex interactome. BMC Systems Biology, 8 Suppl 4(Suppl 4), S11. https://doi.org/10.1186/1752-0509-8-S4-S11
   PubMedGoogle Scholar
• Clark, A. M., & Labute, P. (2007). 2D depiction of protein − ligand complexes. Journal of Chemical Information and Modeling, 47(5), 1933–1944. https://doi.org/10.1021/ci7001473
   PubMed Web of Science ®Google Scholar
• Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7(1), 42717. https://doi.org/10.1038/srep42717
   PubMed Web of Science ®Google Scholar
• Demir, S., Tinmaz, F., Dege, N., & Ilhan, I. O. (2016). Vibrational spectroscopic studies, NMR, HOMO–LUMO, NLO and NBO analysis of 1-(2-nitrobenzoyl)-3, 5-diphenyl-4, 5-dihydro-1H-pyrazole with use X-ray diffractions and DFT calculations. Journal of Molecular Structure, 1108, 637–648. https://doi.org/10.1016/j.molstruc.2015.12.057
   Web of Science ®Google Scholar
• Diallo, A., & Prigent, C. (2011). The serine/threonine kinases that control cell cycle progression as therapeutic targets. Bulletin du Cancer, 98(11), 1335–1345. https://doi.org/10.1684/bdc.2011.1467
   PubMed Web of Science ®Google Scholar
• Ding, L., Cao, J., Lin, W., Chen, H., Xiong, X., Ao, H., Yu, M., Lin, J., & Cui, Q. (2020). The roles of cyclin-dependent kinases in cell-cycle progression and therapeutic strategies in human breast cancer. International Journal of Molecular Sciences, 21(6), 1960. https://doi.org/10.3390/ijms21061960
   PubMed Web of Science ®Google Scholar
• Eldehna, W. M., El Hassab, M. A., Abo-Ashour, M. F., Al-Warhi, T., Elaasser, M. M., Safwat, N. A., Suliman, H., Ahmed, M. F., Al-Rashood, S. T., Abdel-Aziz, H. A., & El-Haggar, R. (2021). Development of isatin-thiazolo [3, 2-a] benzimidazole hybrids as novel CDK2 inhibitors with potent in vitro apoptotic anti-proliferative activity: Synthesis, biological and molecular dynamics investigations. Bioorganic Chemistry, 110, 104748. https://doi.org/10.1016/j.bioorg.2021.104748
   PubMed Web of Science ®Google Scholar
• Genheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery, 10(5), 449–461. https://doi.org/10.1517/17460441.2015.1032936
   PubMed Web of Science ®Google Scholar
• Grasso, S., De Sarro, G., De Sarro, A., Micale, N., Zappalà, M., Puia, G., Baraldi, M., & De Micheli, C. (1999). Synthesis and anticonvulsant activity of novel and potent 2, 3-benzodiazepine AMPA/kainate receptor antagonists. Journal of Medicinal Chemistry, 42(21), 4414–4421. https://doi.org/10.1021/jm991086d
   PubMed Web of Science ®Google Scholar
• Guedes, I. A., de Magalhães, C. S., & Dardenne, L. E. (2014). Receptor–ligand molecular docking. Biophysical Reviews, 6(1), 75–87. https://doi.org/10.1007/s12551-013-0130-2
   PubMedGoogle Scholar
• Harder, E., Damm, W., Maple, J., Wu, C., Reboul, M., Xiang, J. Y., Wang, L., Lupyan, D., Dahlgren, M. K., Knight, J. L., Kaus, J. W., Cerutti, D. S., Krilov, G., Jorgensen, W. L., Abel, R., & Friesner, R. A. (2016). OPLS3: A force field providing broad coverage of drug-like small molecules and proteins. Journal of Chemical Theory and Computation, 12(1), 281–296. https://doi.org/10.1021/acs.jctc.5b00864
   PubMed Web of Science ®Google Scholar
• 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), 1000.
   Google Scholar
• Johnson, L. N., De Moliner, E., Brown, N. R., Song, H., Barford, D., Endicott, J. A., & Noble, M. E. M. (2002). Structural studies with inhibitors of the cell cycle regulatory kinase cyclin-dependent protein kinase 2. Pharmacology & Therapeutics, 93(2-3), 113–124. https://doi.org/10.1016/s0163-7258(02)00181-x
   PubMed Web of Science ®Google Scholar
• Kagami, L. P., das Neves, G. M., Timmers, L. F. S. M., Caceres, R. A., & Eifler-Lima, V. L. (2020). Geo-Measures: A PyMOL plugin for protein structure ensembles analysis. Computational Biology and Chemistry, 87, 107322. https://doi.org/10.1016/j.compbiolchem.2020.107322
   PubMed Web of Science ®Google Scholar
• Kamal, A., Shetti, R. V. C. R. N. C., Ramaiah, M. J., Swapna, P., Reddy, K. S., Mallareddy, A., Rao, M. P. N., Chourasia, M., Sastry, G. N., Juvekar, A., Zingde, S., Sarma, P., Pushpavalli, S. N. C. V. L., & Pal-Bhadra, M. (2011). Carbazole–pyrrolo [2, 1-c][1, 4] benzodiazepine conjugates: Design, synthesis, and biological evaluation. MedChemComm, 2(8), 780–788. https://doi.org/10.1039/c1md00072a
   Web of Science ®Google Scholar
• Kamal, A., Vijaya Bharathi, E., Janaki Ramaiah, M., Dastagiri, D., Surendranadha Reddy, J., Viswanath, A., Sultana, F., Pushpavalli, S. N. C. V. L., Pal-Bhadra, M., Srivastava, H. K., Narahari Sastry, G., Juvekar, A., Sen, S., & Zingde, S. (2010). Quinazolinone linked pyrrolo [2, 1-c][1, 4] benzodiazepine (PBD) conjugates: Design, synthesis and biological evaluation as potential anticancer agents. Bioorganic & Medicinal Chemistry, 18(2), 526–542. https://doi.org/10.1016/j.bmc.2009.12.015
   PubMed Web of Science ®Google Scholar
• Kontopidis, G., McInnes, C., Pandalaneni, S. R., McNae, I., Gibson, D., Mezna, M., Thomas, M., Wood, G., Wang, S., Walkinshaw, M. D., & Fischer, P. M. (2006). Differential binding of inhibitors to active and inactive CDK2 provides insights for drug design. Chemistry & Biology, 13(2), 201–211. https://doi.org/10.1016/j.chembiol.2005.11.011
   PubMedGoogle Scholar
• Kuleshov, M. V., Jones, M. R., Rouillard, A. D., Fernandez, N. F., Duan, Q., Wang, Z., Koplev, S., Jenkins, S. L., Jagodnik, K. M., Lachmann, A., McDermott, M. G., Monteiro, C. D., Gundersen, G. W., & Ma’ayan, A. (2016). Enrichr: A comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Research, 44(W1), W90–W97. https://doi.org/10.1093/nar/gkw377
   PubMed Web of Science ®Google Scholar
• Kumar, C. P., Reddy, T. S., Mainkar, P. S., Bansal, V., Shukla, R., Chandrasekhar, S., & Hügel, H. M. (2016). Synthesis and biological evaluation of 5, 10-dihydro-11H-dibenzo [b, e][1, 4] diazepin-11-one structural derivatives as anti-cancer and apoptosis inducing agents. European Journal of Medicinal Chemistry, 108, 674–686. https://doi.org/10.1016/j.ejmech.2015.12.007
   PubMed Web of Science ®Google Scholar
• Legler, C. R., Brown, N. R., Dunbar, R. A., Harness, M. D., Nguyen, K., Oyewole, O., & Collier, W. B. (2015). Scaled quantum mechanical scale factors for vibrational calculations using alternate polarized and augmented basis sets with the B3LYP density functional calculation model. Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy, 145, 15–24. https://doi.org/10.1016/j.saa.2015.02.103
   PubMed Web of Science ®Google Scholar
• Lipinski, C. A. (2004). Lead-and drug-like compounds: The rule-of-five revolution. Drug Discovery Today. Technologies, 1(4), 337–341. https://doi.org/10.1016/j.ddtec.2004.11.007
   PubMedGoogle Scholar
• Maaser, K., Sutter, A. P., Krahn, A., Höpfner, M., Grabowski, P., & Scherübl, H. (2004). Cell cycle-related signaling pathways modulated by peripheral benzodiazepine receptor ligands in colorectal cancer cells. Biochemical and Biophysical Research Communications, 324(2), 878–886. https://doi.org/10.1016/j.bbrc.2004.09.127
   PubMed Web of Science ®Google Scholar
• Malumbres, M., & Barbacid, M. (2009). Cell cycle, CDKs and cancer: A changing paradigm. Nature Reviews. Cancer, 9(3), 153–166. https://doi.org/10.1038/nrc2602
   PubMed Web of Science ®Google Scholar
• Meng, X.-Y., Zhang, H.-X., Mezei, M., & Cui, M. (2011). Molecular docking: A powerful approach for structure-based drug discovery. Current Computer-Aided Drug Design, 7(2), 146–157. https://doi.org/10.2174/157340911795677602
   PubMed Web of Science ®Google Scholar
• Miduturu, C. V., Deng, X., Kwiatkowski, N., Yang, W., Brault, L., Filippakopoulos, P., Chung, E., Yang, Q., Schwaller, J., Knapp, S., King, R. W., Lee, J.-D., Herrgard, S., Zarrinkar, P., & Gray, N. S. (2011). High-throughput kinase profiling: A more efficient approach toward the discovery of new kinase inhibitors. Chemistry & Biology, 18(7), 868–879. https://doi.org/10.1016/j.chembiol.2011.05.010
   PubMed Web of Science ®Google Scholar
• Mohan, N., & Suresh, C. H. (2014). A molecular electrostatic potential analysis of hydrogen, halogen, and dihydrogen bonds. The Journal of Physical Chemistry. A, 118(9), 1697–1705. https://doi.org/10.1021/jp4115699
   PubMed Web of Science ®Google Scholar
• Mughal, M. J., Bhadresha, K., & Kwok, H. F. (2023). CDK inhibitors from past to present: A new wave of cancer therapy. In Seminars in Cancer Biology (Vol. 88, pp. 106–122). Academic Press.
   Google Scholar
• Padma, V. V. (2015). An overview of targeted cancer therapy. BioMedicine, 5(4), 19. https://doi.org/10.7603/s40681-015-0019-4
   PubMedGoogle Scholar
• Pan, B., Zhong, W., Deng, Z., Lai, C., Chu, J., Jiao, G., Liu, J., & Zhou, Q. (2016). Inhibition of prostate cancer growth by solanine requires the suppression of cell cycle proteins and the activation of ROS/P38 signaling pathway. Cancer Medicine, 5(11), 3214–3222. https://doi.org/10.1002/cam4.916
   PubMed Web of Science ®Google Scholar
• Peyressatre, M., Prével, C., Pellerano, M., & Morris, M. C. (2015). Targeting cyclin-dependent kinases in human cancers: From small molecules to peptide inhibitors. Cancers, 7(1), 179–237. https://doi.org/10.3390/cancers7010179
   PubMed Web of Science ®Google Scholar
• Rahman, K. M., Jackson, P. J. M., James, C. H., Basu, B. P., Hartley, J. A., de la Fuente, M., Schatzlein, A., Robson, M., Pedley, R. B., Pepper, C., Fox, K. R., Howard, P. W., & Thurston, D. E. (2013). GC-targeted C8-linked pyrrolobenzodiazepine–biaryl conjugates with femtomolar in vitro cytotoxicity and in vivo antitumor activity in mouse models. Journal of Medicinal Chemistry, 56(7), 2911–2935. https://doi.org/10.1021/jm301882a
   PubMed Web of Science ®Google Scholar
• Rahman, A. A. H. A., Nassar, I. F., Shaban, A. K. F., El-Kady, D. S., Awad, H. M., & El Sayed, W. A. (2019). Synthesis, docking studies into CDK-2 and anticancer activity of new derivatives based pyrimidine scaffold and their derived glycosides. Mini Reviews in Medicinal Chemistry, 19(13), 1093–1110. https://doi.org/10.2174/1389557519666190312165717
   PubMed Web of Science ®Google Scholar
• S. Release. (2021). 1: Desmond Molecular Dynamics System, DE Shaw Research., Maestro-Desmond Interoperability Tools, Schrödinger. 2023.
   Google Scholar
• Sabe, V. T., Ntombela, T., Jhamba, L. A., Maguire, G. E. M., Govender, T., Naicker, T., & Kruger, H. G. (2021). Current trends in computer aided drug design and a highlight of drugs discovered via computational techniques: A review. European Journal of Medicinal Chemistry, 224, 113705. https://doi.org/10.1016/j.ejmech.2021.113705
   PubMed Web of Science ®Google Scholar
• Saifi, I., Bhat, B. A., Hamdani, S. S., Bhat, U. Y., Lobato-Tapia, C. A., Mir, M. A., Dar, T. U. H., & Ganie, S. A. (2023). Artificial intelligence and cheminformatics tools: A contribution to the drug development and chemical science. Journal of Biomolecular Structure & Dynamics, 6, 1–19. https://doi.org/10.1080/07391102.2023.2234039
   Google Scholar
• Sajjan, V. P., Anigol, L. B., Gurubasavaraj, P. M., Patil, D., Patil, P. S., Gummagol, N. B., Quah, C. K., Wong, Q. A., & Celik, I. (2023). New2-((2-(2, 4-dinitrophenyl) hydrazineeylidene) derivatives: Design, synthesis, in silico, and in vitro anticancer studies. Journal of Biomolecular Structure and Dynamics, 41(21), 11681–11699.
   PubMed Web of Science ®Google Scholar
• Siegel, R. L., Miller, K. D., Fuchs, H. E., & Jemal, A. (2021). Cancer statistics. CA: A Cancer Journal for Clinicians, 71(1), 7–33. https://doi.org/10.3322/caac.21654
   PubMed Web of Science ®Google Scholar
• Tadesse, S., Caldon, E. C., Tilley, W., & Wang, S. (2018). Cyclin-dependent kinase 2 inhibitors in cancer therapy: An update. Journal of Medicinal Chemistry, 62(9), 4233–4251. https://doi.org/10.1021/acs.jmedchem.8b01469
   PubMed Web of Science ®Google Scholar
• Tirado-Rives, J., & Jorgensen, W. L. (2008). Performance of B3LYP density functional methods for a large set of organic molecules. Journal of Chemical Theory and Computation, 4(2), 297–306. https://doi.org/10.1021/ct700248k
   PubMed Web of Science ®Google Scholar
• Tolu-Bolaji, O. O., Sojinu, S. O., Okedere, A. P., & Ajani, O. O. (2022). A review on the chemistry and pharmacological properties of benzodiazepine motifs in drug design. Arab Journal of Basic and Applied Sciences, 29(1), 287–306. https://doi.org/10.1080/25765299.2022.2117677
   Google Scholar
• Topcul, M., & Cetin, I. (2014). Endpoint of cancer treatment: Targeted therapies. Asian Pacific Journal of Cancer Prevention, 15(11), 4395–4403. https://doi.org/10.7314/apjcp.2014.15.11.4395
   PubMedGoogle Scholar
• Van Meerloo, J., Kaspers, G. J. L., & Cloos, J. (2011). Cell sensitivity assays: The MTT assay, Cancer cell culture: Methods and protocols. 237–245.
   Google Scholar
• Verma, D., Kumar, P., Narasimhan, B., Ramasamy, K., Mani, V., Mishra, R. K., & Majeed, A. B. A. (2019). Synthesis, antimicrobial, anticancer and QSAR studies of 1-[4-(substituted phenyl)-2-(substituted phenyl azomethyl)-benzo [b]-[1, 4] diazepin-1-yl]-2-substituted phenylaminoethanones. Arabian Journal of Chemistry, 12(8), 2882–2896. https://doi.org/10.1016/j.arabjc.2015.06.010
   Web of Science ®Google Scholar
• Wang, L.-Z., Li, X.-Q., & An, Y.-S. (2015). 1, 5-Benzodiazepine derivatives as potential antimicrobial agents: Design, synthesis, biological evaluation, and structure–activity relationships. Organic & Biomolecular Chemistry, 13(19), 5497–5509. https://doi.org/10.1039/c5ob00655d
   PubMed Web of Science ®Google Scholar
• Wang, S., Liu, Y., Feng, Y., Zhang, J., Swinnen, J., Li, Y., & Ni, Y. (2019). A review on curability of cancers: More efforts for novel therapeutic options are needed. Cancers, 11(11), 1782. https://doi.org/10.3390/cancers11111782
   PubMed Web of Science ®Google Scholar
• Zhang, M., Zhang, L., Hei, R., Li, X., Cai, H., Wu, X., Zheng, Q., & Cai, C. (2021). CDK inhibitors in cancer therapy, an overview of recent development. American Journal of Cancer Research, 11(5), 1913.
   PubMed Web of Science ®Google Scholar