130
Views
0
CrossRef citations to date
0
Altmetric
Research Article

In silico research on new sulfonamide derivatives as BRD4 inhibitors targeting acute myeloid leukemia using various computational techniques including 3D-QSAR, HQSAR, molecular docking, ADME/Tox, and molecular dynamics

, , , , , & show all
Received 20 Jun 2023, Accepted 15 Aug 2023, Published online: 01 Sep 2023

References

  • Abdullahi, M., Uzairu, A., Shallangwa, G. A., Mamza, P. A., Ibrahim, M. T., Ahmad, I., & Patel, H. (2023). Structure-based drug design, molecular dynamics simulation, ADMET, and quantum chemical studies of some thiazolinones targeting influenza neuraminidase. Journal of Biomolecular Structure & Dynamics, 1–15. https://doi.org/10.1080/07391102.2023.2208225
  • Anand, A., Ghosh, P., Singh, R., Gajanan Bajad, N., Kumar, A., & Singh, S. K. (2023). Identification of potent histone deacetylase 2 (HDAC2) inhibitors through combined structure and ligand-based designs and molecular modelling approach. Journal of Biomolecular Structure & Dynamics, 1–20. https://doi.org/10.1080/07391102.2023.2222177
  • Ash, J., & Fourches, D. (2017). Characterizing the chemical space of ERK2 kinase inhibitors using descriptors computed from molecular dynamics trajectories. Journal of Chemical Information and Modeling, 57(6), 1286–1299. https://doi.org/10.1021/acs.jcim.7b00048
  • Belghalia, E., Bahi, S. E., Ouabane, M., Sbai, A., Lakhlifi, T., & Bouachrine, M. (2022). 4-phenoxypyridine derivatives containing imidazole -4- carboxamide and 1,2,4- triazole -3- carboxamide moieties as powerful antitumor agents. QSAR Studies, Rhazes, 16, 33-45. https://doi.org/10.48419/IMIST.PRSM/rhazes-v16.35251
  • Bouamrane, S., Khaldan, A., Hajji, H., El-Mernissi, R., Alaqarbeh, M., Alsakhen, N., Maghat, H., Ajana, M. A., Sbai, A., Bouachrine, M., & Lakhlifi, T. (2022). In silico identification of 1,2,4-triazoles as potential Candida Albicans inhibitors using 3D-QSAR, molecular docking, molecular dynamics simulations, and ADMET profiling. Molecular Diversity, https://doi.org/10.1007/s11030-022-10546-x
  • Bowers, K. J., Chow, D. E., Xu, H., Dror, R. O., Eastwood, M. P., Gregersen, B. A., Klepeis, J. L., Kolossvary, I., Moraes, M. A., Sacerdoti, F. D., Salmon, J. K., Shan, Y., & Shaw, D. E. (2006). Scalable algorithms for molecular dynamics simulations on commodity clusters [Paper presentation]. ACM/IEEE SC 2006 Conference (SC’06), pp. 43–43. https://doi.org/10.1109/SC.2006.54
  • Burnett, A., Wetzler, M., & Löwenberg, B. (2011). Therapeutic advances in acute myeloid leukemia. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology, 29(5), 487–494. https://doi.org/10.1200/JCO.2010.30.1820
  • Cabezas, D., Mellado, G., Espinoza, N., Gárate, J. A., Morales, C., Castro-Alvarez, A., Matos, M. J., Mellado, M., & Mella, J. (2023). In silico approaches to develop new phenyl-pyrimidines as glycogen synthase kinase 3 (GSK-3) inhibitors with halogen-bonding capabilities: 3D-QSAR CoMFA/CoMSIA, molecular docking and molecular dynamics studies. Journal of Biomolecular Structure & Dynamics, 1–10. https://doi.org/10.1080/07391102.2023.2172457
  • Chhatbar, D. M., Chaube, U. J., Vyas, V. K., & Bhatt, H. G. (2019). CoMFA, CoMSIA, Topomer CoMFA, HQSAR, molecular docking and molecular dynamics simulations study of triazine morpholino derivatives as mTOR inhibitors for the treatment of breast cancer. Computational Biology and Chemistry, 80, 351–363. https://doi.org/10.1016/j.compbiolchem.2019.04.017
  • Chien, L.-N., Tzeng, H.-E., Liu, H.-Y., Chou, W.-C., Tien, H.-F., & Hou, H.-A. (2023). Epidemiology and survival outcomes of acute myeloid leukemia patients in Taiwan: A national population-based analysis from 2001 to 2015. Journal of the Formosan Medical Association = Taiwan yi Zhi, 122(6), 505–513. https://doi.org/10.1016/j.jfma.2022.10.007
  • Döhner, H., Weisdorf, D. J., & Bloomfield, C. D. (2015). Acute myeloid leukemia. The New England Journal of Medicine, 373(12), 1136–1152. https://doi.org/10.1056/NEJMra1406184
  • El Khatabi, K., Kumar, S., El-Mernissi, R., Singh, A. K., Ajana, M. A., Lakhlifi, T., & Bouachrine, M. (2022). Novel Eubacterium rectale inhibitor from Coriandrum sativum L. for possible prevention of colorectal cancer: A computational approach. Journal of Biomolecular Structure & Dynamics, 1–15. https://doi.org/10.1080/07391102.2022.2134210
  • Feng, Z., Chen, A., Shi, J., Zhou, D., Shi, W., Qiu, Q., Liu, X., Huang, W., Li, J., Qian, H., & Zhang, W. (2021). Design, synthesis, and biological activity evaluation of a series of novel sulfonamide derivatives as BRD4 inhibitors against acute myeloid leukemia. Bioorganic Chemistry, 111, 104849. https://doi.org/10.1016/j.bioorg.2021.104849
  • Ghobadi, E., Hashemi, S. M., Fakhim, H., Hosseini-Khah, Z., Badali, H., & Emami, S. (2023). Design, synthesis and biological activity of hybrid antifungals derived from fluconazole and mebendazole. European Journal of Medicinal Chemistry, 249, 115146. https://doi.org/10.1016/j.ejmech.2023.115146
  • Heidari, A., & Fatemi, M. H. (2017). Comparative molecular field analysis (CoMFA), topomer CoMFA, and hologram QSAR studies on a series of novel HIV-1 protease inhibitors. Chemical Biology & Drug Design, 89(6), 918–931. https://doi.org/10.1111/cbdd.12917
  • Jia, Q., Zhao, Y., Yan, F., & Wang, Q. (2018). QSAR model for predicting the toxicity of organic compounds to fathead minnow. Environmental Science and Pollution Research International, 25(35), 35420–35428. https://doi.org/10.1007/s11356-018-3434-8
  • Jin, W., Tan, H., Wu, J., He, G., & Liu, B. (2022). Dual-target inhibitors of bromodomain-containing protein 4 (BRD4) in cancer therapy: Current situation and future directions. Drug Discovery Today, 27(1), 246–256. https://doi.org/10.1016/j.drudis.2021.08.007
  • Joshi, S. D., More, U. A., Aminabhavi, T. M., & Badiger, A. M. (2014). Two- and three-dimensional QSAR studies on a set of antimycobacterial pyrroles: CoMFA, Topomer CoMFA, and HQSAR. Medicinal Chemistry Research, 23(1), 107–126. https://doi.org/10.1007/s00044-013-0607-3
  • Kadi, I., Eltayb, W. A., Boufissiou, A., Benaceur, F., Bouchareb, A., Soltan, W. B., Baladehi, M. H., Kheniche, A., & Abdalla, M. (2023). Molecular interactions, binding stability, and synergistic inhibition on Acetylcholinesterase activity of Safranin O in combination with Quercetin and Gallic acid: In vitro and in silico study. Journal of Molecular Structure, 1286, 135562. https://doi.org/10.1016/j.molstruc.2023.135562
  • Kardile, R. A., Sarkate, A. P., Lokwani, D. K., Tiwari, S. V., Azad, R., & Thopate, S. R. (2023). Design, synthesis, and biological evaluation of novel quinoline derivatives as small molecule mutant EGFR inhibitors targeting resistance in NSCLC: In vitro screening and ADME predictions. European Journal of Medicinal Chemistry, 245(Pt 1), 114889. https://doi.org/10.1016/j.ejmech.2022.114889
  • Khan, K., Albalawi, K., Abbas, M. N., Burki, S., Musad Saleh, E. A., Al Mouslem, A., Alsaiari, A. A. A., Zaki, M. E., Khan, A. U., Alotaibi, G., & Jalal, K. (2023). Pharmacokinetics and drug-likeness of anti-cancer traditional Chinese medicine: Molecular docking and molecular dynamics simulation study. Journal of Biomolecular Structure & Dynamics, 1–12. https://doi.org/10.1080/07391102.2023.2216758
  • Kirchmair, J., Markt, P., Distinto, S., Wolber, G., & Langer, T. (2008). Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection—What can we learn from earlier mistakes? Journal of Computer-Aided Molecular Design, 22(3–4), 213–228. https://doi.org/10.1007/s10822-007-9163-6
  • Kouranov, A., Xie, L., de la Cruz, J., Chen, L., Westbrook, J., Bourne, P. E., & Berman, H. M. (2006). The RCSB PDB information portal for structural genomics. Nucleic Acids Research, 34, D302–D305. https://doi.org/10.1093/nar/gkj120
  • Liang, D., Yu, Y., & Ma, Z. (2020). Novel strategies targeting bromodomain-containing protein 4 (BRD4) for cancer drug discovery. European Journal of Medicinal Chemistry, 200, 112426. https://doi.org/10.1016/j.ejmech.2020.112426
  • Liu, J., Feng, K., & Ren, Y. (2019). In silico studies on potential TNKS inhibitors: A combination of pharmacophore and 3D-QSAR modelling, virtual screening, molecular docking and molecular dynamics. Journal of Biomolecular Structure & Dynamics, 37(14), 3803–3821. https://doi.org/10.1080/07391102.2018.1528887
  • Luna, I. S., Souza, T. A. D., da Silva, M. S., Franca Rodrigues, K. A. D., Scotti, L., Scotti, M. T., & Mendonça-Junior, F. J. B. (2023). Computer-Aided drug design of new 2-amino-thiophene derivatives as anti-leishmanial agents. European Journal of Medicinal Chemistry, 250, 115223. https://doi.org/10.1016/j.ejmech.2023.115223
  • Ma, C., Liu, W., Liu, W., Xi, C., Xiong, F., & Zhang, S. (2022). Molecular docking and 3D-QSAR studies on a series of benzenesulfonamide derivatives as a Hepatitis B virus capsid assembly inhibitor. Polycyclic Aromatic Compounds, 42(6), 3622–3637. https://doi.org/10.1080/10406638.2020.1871038
  • Matin, M. M., Hasan, M. S., Uzzaman, M., Bhuiyan, M. M. H., Kibria, S. M., Hossain, M. E., & Roshid, M. H. O. (2020). Synthesis, spectroscopic characterization, molecular docking, and ADMET studies of mannopyranoside esters as antimicrobial agents. Journal of Molecular Structure, 1222, 128821. https://doi.org/10.1016/j.molstruc.2020.128821
  • Mirguet, O., Lamotte, Y., Donche, F., Toum, J., Gellibert, F., Bouillot, A., Gosmini, R., Nguyen, V.-L., Delannée, D., Seal, J., Blandel, F., Boullay, A.-B., Boursier, E., Martin, S., Brusq, J.-M., Krysa, G., Riou, A., Tellier, R., Costaz, A., … Nicodeme, E. (2012). From ApoA1 upregulation to BET family bromodomain inhibition: Discovery of I-BET151. Bioorganic & Medicinal Chemistry Letters, 22(8), 2963–2967. https://doi.org/10.1016/j.bmcl.2012.01.125
  • Patel, A., Bhatt, H., & Patel, B. (2022). Structural insights on 2-phenylquinazolin-4-one derivatives as tankyrase inhibitors through CoMFA, CoMSIA, topomer CoMFA and HQSAR studies. Journal of Molecular Structure, 1249, 131636. https://doi.org/10.1016/j.molstruc.2021.131636
  • Picaud, S., Da Costa, D., Thanasopoulou, A., Filippakopoulos, P., Fish, P. V., Philpott, M., Fedorov, O., Brennan, P., Bunnage, M. E., Owen, D. R., Bradner, J. E., Taniere, P., O'Sullivan, B., Müller, S., Schwaller, J., Stankovic, T., & Knapp, S. (2013). PFI-1, a highly selective protein interaction inhibitor, targeting BET bromodomains. Cancer Research, 73(11), 3336–3346. https://doi.org/10.1158/0008-5472.CAN-12-3292
  • Rajaraman, D., Anthony, L. A., Nethaji, P., & Vallangi, R. (2023). One-pot synthesis, NMR, quantum chemical approach, molecular docking studies, drug-likeness and in-silico ADMET prediction of novel 1-(2,3-dihydrobenzo[b][1,4]dioxin-6-yl)-2-(furan-2-yl)-4,5-diphenyl-1H-imidazole derivatives. Journal of Molecular Structure, 1273, 134314. https://doi.org/10.1016/j.molstruc.2022.134314
  • Rehman, H. M., Sajjad, M., Ali, M. A., Gul, R., Irfan, M., Naveed, M., Bhinder, M. A., Ghani, M. U., Hussain, N., Said, A. S. A., Al Haddad, A. H. I., & Saleem, M. (2023a). Identification of NS2B-NS3 protease inhibitors for therapeutic application in ZIKV infection: A pharmacophore-based high-throughput virtual screening and MD simulations approaches. Vaccines, 11(1), 131. https://doi.org/10.3390/vaccines11010131
  • Rehman, H. M., Sajjad, M., Ali, M. A., Gul, R., Naveed, M., Aslam, M. S., Shinwari, K., Bhinder, M. A., Ghani, M. U., Saleem, M., Rather, M. A., Ahmad, I., & Amin, A. (2023b). Identification of RdRp inhibitors against SARS-CoV-2 through E-pharmacophore-based virtual screening, molecular docking and MD simulations approaches. International Journal of Biological Macromolecules, 237, 124169. https://doi.org/10.1016/j.ijbiomac.2023.124169
  • Seal, J., Lamotte, Y., Donche, F., Bouillot, A., Mirguet, O., Gellibert, F., Nicodeme, E., Krysa, G., Kirilovsky, J., Beinke, S., McCleary, S., Rioja, I., Bamborough, P., Chung, C.-W., Gordon, L., Lewis, T., Walker, A. L., Cutler, L., Lugo, D., … Prinjha, R. K. (2012). Identification of a novel series of BET family bromodomain inhibitors: Binding mode and profile of I-BET151 (GSK1210151A). Bioorganic & Medicinal Chemistry Letters, 22(8), 2968–2972. https://doi.org/10.1016/j.bmcl.2012.02.041
  • Sengupta, S., Bhowmik, R., Acharjee, S., & Sen, S. (2021). http://www.biotech-asia.org/vol18no2/in-silico-modelling-of-1-3-3-substituted-phenyl-prop-2-enoyl-phenyl-thiourea-against-anti-inflammatory-drug-targets/. Biosciences Biotechnology Research Asia, 18(2), 413–421. https://doi.org/10.13005/bbra/2928
  • Siegel, R. L., Miller, K. D., & Jemal, A. (2019). Cancer statistics, 2019. CA: A Cancer Journal for Clinicians, 69(1), 7–34. https://doi.org/10.3322/caac.21551
  • Singh, H. L., Dhingra, N., & Bhanuka, S. (2023). Synthesis, spectral, antibacterial and QSAR studies of tin and silicon complexes with Schiff base of amino acids. Journal of Molecular Structure, 1287, 135670. https://doi.org/10.1016/j.molstruc.2023.135670
  • Srivani, P., & Sastry, G. N. (2009). Potential choline kinase inhibitors: A molecular modeling study of bis-quinolinium compounds. Journal of Molecular Graphics & Modelling, 27(6), 676–688. https://doi.org/10.1016/j.jmgm.2008.10.010
  • Tabti, K., Baammi, S., Sbai, A., Maghat, H., Lakhlifi, T., & Bouachrine, M. (2023). Molecular modeling study of pyrrolidine derivatives as novel myeloid cell leukemia-1 inhibitors through combined 3D-QSAR, molecular docking, ADME/Tox and MD simulation techniques. Journal of Biomolecular Structure & Dynamics, 1–17. https://doi.org/10.1080/07391102.2023.2183032
  • Tabti, K., Elmchichi, L., Sbai, A., Maghat, H., Bouachrine, M., & Lakhlifi, T. (2022a). HQSAR, CoMFA, CoMSIA docking studies and simulation MD on quinazolines/quinolines derivatives for DENV virus inhibitory activity. Chemistry Africa, 5(6), 1937–1958. https://doi.org/10.1007/s42250-022-00484-4
  • Tabti, K., Elmchichi, L., Sbai, A., Maghat, H., Bouachrine, M., Lakhlifi, T., & Ghosh, A. (2022b). In silico design of novel PIN1 inhibitors by combined of 3D-QSAR, molecular docking, molecular dynamic simulation and ADMET studies. Journal of Molecular Structure, 1253 (2022), 132291. https://doi.org/10.1016/j.molstruc.2021.132291
  • Tallman, M. S., Gilliland, D. G., & Rowe, J. M. (2005). Drug therapy for acute myeloid leukemia. Blood, 106(4), 1154–1163. https://doi.org/10.1182/blood-2005-01-0178
  • Vyas, V. K., Bhatt, H. G., Patel, P. K., Jalu, J., Chintha, C., Gupta, N., & Ghate, M. (2013). CoMFA and CoMSIA studies on C -aryl glucoside SGLT2 inhibitors as potential anti-diabetic agents. SAR and QSAR in Environmental Research, 24(7), 519–551. https://doi.org/10.1080/1062936X.2012.751553
  • Wang, H., Wang, H., Zhang, J., Luo, J., Peng, C., Tong, X., & Chen, X. (2022). Molecular mechanism of crataegi folium and alisma rhizoma in the treatment of dyslipidemia based on network pharmacology and molecular docking. Evidence-Based Complementary and Alternative Medicine : eCAM, 2022, 4891370. https://doi.org/10.1155/2022/4891370
  • Wang, L., Pratt, J. K., Soltwedel, T., Sheppard, G. S., Fidanze, S. D., Liu, D., Hasvold, L. A., Mantei, R. A., Holms, J. H., McClellan, W. J., Wendt, M. D., Wada, C., Frey, R., Hansen, T. M., Hubbard, R., Park, C. H., Li, L., Magoc, T. J., Albert, D. H., … McDaniel, K. F. (2017). Fragment-based, structure-enabled discovery of novel pyridones and pyridone macrocycles as potent bromodomain and extra-terminal domain (BET) family bromodomain inhibitors. Journal of Medicinal Chemistry, 60(9), 3828–3850. https://doi.org/10.1021/acs.jmedchem.7b00017
  • Xu, W., Hu, B., Cheng, Y., Guo, Y., Yao, W., & Qian, H. (2022). Material basis research for Echinacea purpurea (L.) Moench against hepatocellular carcinoma in a mouse model through integration of metabonomics and molecular docking. Phytomedicine : International Journal of Phytotherapy and Phytopharmacology, 98, 153948. https://doi.org/10.1016/j.phymed.2022.153948
  • Zhang, C., Su, Z.-Y., Wang, L., Shu, L., Yang, Y., Guo, Y., Pung, D., Bountra, C., & Kong, A.-N. (2016). Epigenetic blockade of neoplastic transformation by bromodomain and extra-terminal (BET) domain protein inhibitor JQ-1. Biochemical Pharmacology, 117, 35–45. https://doi.org/10.1016/j.bcp.2016.08.009
  • Zhang, Y., Chen, L., Wang, Z., Zhu, Y., Jiang, H., Xu, J., & Xiong, F. (2023). Design of novel DABO derivatives as HIV-1 RT inhibitors using molecular docking, molecular dynamics simulations and ADMET properties. Journal of Biomolecular Structure & Dynamics, 1–18. https://doi.org/10.1080/07391102.2023.2219331
  • Zhao, Y., Yang, C.-Y., & Wang, S. (2013). The making of I-BET762, a BET bromodomain inhibitor now in clinical development. Journal of Medicinal Chemistry, 56(19), 7498–7500. https://doi.org/10.1021/jm4014407

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.