References
- Abdessadak, O., Koubi, Y., Lakhlifi, T., Ajana, M. A., & Bouachrine, M. (2021). 2D-QSAR study for a series of compounds including the basic molecule [1, 2, 4] Triazolo [1, 5-a] pyrimidine, having anticancer activity. Journal of Analytical Sciences and Applied Biotechnology, 3(1), 20–26. https://doi.org/10.48402/IMIST.PRSM/jasab-v3i1.25363
- Aichberger, K. J., Mayerhofer, M., Krauth, M.-T., Skvara, H., Florian, S., Sonneck, K., Akgul, C., Derdak, S., Pickl, W. F., & Wacheck, V. (2005). Identification of mcl-1 as a BCR/ABL-dependent target in chronic myeloid leukemia (CML) : Evidence for cooperative antileukemic effects of imatinib and mcl-1 antisense oligonucleotides. Blood, 105(8), 3303–3311. https://doi.org/10.1182/blood-2004-02-0749
- Alvarez, P. A., & Pahissa, J. (2010). QT alterations in psychopharmacology : Proven candidates and suspects. Current Drug Safety, 5(1), 97–104.
- Aronov, A. M. (2005). Predictive in silico modeling for hERG channel blockers. Drug Discovery Today, 10(2), 149–155.
- Baker, N. A., Sept, D., Joseph, S., Holst, M. J., & McCammon, J. A. (2001). Electrostatics of nanosystems : Application to microtubules and the ribosome. Proceedings of the National Academy of Sciences of United States of America, 98(18), 10037–10041. https://doi.org/10.1073/pnas.181342398
- Becattini, B., Kitada, S., Leone, M., Monosov, E., Chandler, S., Zhai, D., Kipps, T. J., Reed, J. C., & Pellecchia, M. (2004). Rational design and real time, in-cell detection of the proapoptotic activity of a novel compound targeting Bcl-XL. Chemistry & Biology, 11(3), 389–395. https://doi.org/10.1016/j.chembiol.2004.02.020
- Cheng, F., Li, W., Liu, G., & Tang, Y. (2013). In silico ADMET prediction: Recent advances, current challenges and future trends. Current Topics in Medicinal Chemistry, 13(11), 1273–1289.
- Czabotar, P. E., Lee, E. F., van Delft, M. F., Day, C. L., Smith, B. J., Huang, D. C., Fairlie, W. D., Hinds, M. G., & Colman, P. M. (2007). Structural insights into the degradation of Mcl-1 induced by BH3 domains. Proceedings of the National Academy of Sciences of United States of America, 104(15), 6217–6222. https://doi.org/10.1073/pnas.0701297104
- Czabotar, P. E., Lessene, G., Strasser, A., & Adams, J. M. (2014). Control of apoptosis by the BCL-2 protein family: Implications for physiology and therapy. Nature Reviews Molecular Cell Biology, 15(1), 49–63. https://doi.org/10.1038/nrm3722
- da Paixão, V. G., & da Rocha Pita, S. S. (2019). In silico identification and evaluation of new Trypanosoma cruzi trypanothione reductase (TcTR) inhibitors obtained from natural products database of the Bahia semi-arid region (NatProDB). Computational Biology and Chemistry, 79, 36–47. https://doi.org/10.1016/j.compbiolchem.2019.01.009
- 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), 1–13. https://doi.org/10.1038/srep42717
- Danial, N. N., & Korsmeyer, S. J. (2004). Cell death : Critical control points. Cell, 116(2), 205–219. https://doi.org/10.1016/S0092-8674(04)00046-7
- Degterev, A., Lugovskoy, A., Cardone, M., Mulley, B., Wagner, G., Mitchison, T., & Yuan, J. (2001). Identification of small-molecule inhibitors of interaction between the BH3 domain and Bcl-xL. Nature Cell Biology, 3(2), 173–182. https://doi.org/10.1038/35055085
- El Mchichi, L., Tabti, K., Kasmi, R., El-Mernissi, R., El Aisouq, A., En-Nahli, F., Belhassan, A., Lakhlifi, T., & Bouachrine, M. (2022). 3D-QSAR study, docking molecular and simulation dynamic on series of benzimidazole derivatives as anti-cancer agents. Journal of the Indian Chemical Society, 99(9), 100582. https://doi.org/10.1016/j.jics.2022.100582
- Elmore, S. (2007). Apoptosis : A review of programmed cell death. Toxicologic Pathology, 35(4), 495–516. https://doi.org/10.1080/0192623070132033
- Glaser, S. P., Lee, E. F., Trounson, E., Bouillet, P., Wei, A., Fairlie, W. D., Izon, D. J., Zuber, J., Rappaport, A. R., & Herold, M. J. (2012). Anti-apoptotic Mcl-1 is essential for the development and sustained growth of acute myeloid leukemia. Genes & Development, 26(2), 120–125. https://doi.org/10.1101/gad.182980.111
- Golbraikh, A., & Tropsha, A. (2002). Beware of q2!. Journal of Molecular Graphics and Modelling, 20(4), 269–276. https://doi.org/10.1016/S1093-3263(01)00123-1
- Goldar, S., Khaniani, M. S., Derakhshan, S. M., & Baradaran, B. (2015). Molecular mechanisms of apoptosis and roles in cancer development and treatment. Asian Pacific Journal of Cancer Prevention, 16(6), 2129–2144. https://doi.org/10.7314/APJCP.2015.16.6.2129
- Guo, Y., Xiao, J., Guo, Z., Chu, F., Cheng, Y., & Wu, S. (2005). Exploration of a binding mode of indole amide analogues as potent histone deacetylase inhibitors and 3D-QSAR analyses. Bioorganic & Medicinal Chemistry, 13(18), 5424–5434. https://doi.org/10.1016/j.bmc.2005.05.016
- Hajji, H., Tabti, K., En-Nahli, F., Bouamrane, S., Lakhlifi, T., Ajana, M. A., & Bouachrine, M. (2021). In silico investigation on the beneficial effects of medicinal plants on diabetes and obesity: Molecular docking, molecular dynamic simulations, and ADMET studies. Biointerface research in applied chemistry, 11(5), 6933-6949. https://doi.org/10.33263/BRIAC115.69336949
- Hanahan, D., & Weinberg, R. A. (2011). Hallmarks of cancer: the next generation. Cell, 144(5), 646–674. https://doi.org/10.1016/j.cell.2011.02.013 21376230
- Hess, B., Kutzner, C., Van Der Spoel, D., & Lindahl, E. (2008). GROMACS 4 : Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 4(3), 435–447. https://doi.org/10.1021/ct700301q
- Hou, T., Wang, J., Zhang, W., & Xu, X. (2007). ADME evaluation in drug discovery. 7. Prediction of oral absorption by correlation and classification. Journal of Chemical Information and Modeling, 47(1), 208–218. https://doi.org/10.1021/ci600343x
- Islam, M. T., & Mubarak, M. S. (2020). Pyrrolidine alkaloids and their promises in pharmacotherapy. Advances in Traditional Medicine, 20(1), 13–22. https://doi.org/10.1007/s13596-019-00419-4
- Issa, N. T., Badiavas, E. V., & Schürer, S. (2019). Research techniques made simple: Molecular docking in dermatology-A foray into in silico drug discovery. Journal of Investigative Dermatology, 139(12), 2400–2408. e1 https://doi.org/10.1016/j.jid.2019.06.129
- Jain, A. N. (2003). Surflex : Fully automatic flexible molecular docking using a molecular similarity-based search engine. Journal of Medicinal Chemistry, 46(4), 499–511. https://doi.org/10.1021/jm020406h
- Jain, A. N. (2007). Surflex-Dock 2.1 : Robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search. Journal of Computer-Aided Molecular Design, 21(5), 281–306. https://doi.org/10.1007/s10822-007-9114-2
- Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926–935. https://doi.org/10.1063/1.445869
- Jung, H., Aman, W., & Hah, J.-M. (2017). Novel scaffold evolution through combinatorial 3D-QSAR model studies of two types of JNK3 inhibitors. Bioorganic & Medicinal Chemistry Letters, 27(10), 2139–2143. https://doi.org/10.1016/j.bmcl.2017.03.063
- Kapetanovic, I. (2008). Computer-aided drug discovery and development (CADDD) : In silico-chemico-biological approach. Chemico-Biological Interactions, 171(2), 165–176. https://doi.org/10.1016/j.cbi.2006.12.006
- Kulkarni, S. S., Patel, M. R., & Talele, T. T. (2008). CoMFA and HQSAR studies on 6, 7-dimethoxy-4-pyrrolidylquinazoline derivatives as phosphodiesterase10A inhibitors. Bioorganic & Medicinal Chemistry, 16(7), 3675–3686. https://doi.org/10.1016/j.bmc.2008.02.013
- Kumar, A., Nimsarkar, P., & Singh, S. (2022). Systems pharmacology aiding benzimidazole scaffold as potential lead compounds against leishmaniasis for functional therapeutics. Life Sciences, 308, 120960. https://doi.org/10.1016/j.lfs.2022.120960
- Kumari, R., & Kumar, R. (2014). Consortium OSDD, Lynn A. g_mmpbsa A GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling. 54(7), 1951–1962. https://doi.org/10.1021/ci500020m
- Kutzner, C., Páll, S., Fechner, M., Esztermann, A., de Groot, B. L., & Grubmüller, H. (2019). More bang for your buck : Improved use of GPU nodes for GROMACS 2018. Journal of Computational Chemistry, 40(27), 2418–2431. https://doi.org/10.1002/jcc.26011
- Liu, X. C., Lai, D., Liu, Q. Z., Zhou, L., Liu, Q., & Liu, Z. L. (2016). Bioactivities of a new pyrrolidine alkaloid from the root barks of Orixa japonica. Molecules, 21(12), 1665. https://doi.org/10.3390/molecules21121665
- Malathi, K., & Ramaiah, S. (2016). Molecular docking and molecular dynamics studies to identify potential OXA-10 extended spectrum β-Lactamase non-hydrolysing inhibitors for pseudomonas aeruginosa. Cell Biochemistry and Biophysics, 74(2), 141–155. https://doi.org/10.1007/s12013-016-0735-8
- Montero, J., & Letai, A. (2018). Why do BCL-2 inhibitors work and where should we use them in the clinic? Cell Death and Differentiation, 25(1), 56–64. https://doi.org/10.1038/cdd.2017.183
- Moroy, G., Martiny, V. Y., Vayer, P., Villoutreix, B. O., & Miteva, M. A. (2012). Toward in silico structure-based ADMET prediction in drug discovery. Drug Discovery Today. 17(1–2), 44–55. https://doi.org/10.1016/j.drudis.2011.10.023
- Paschek, D., Day, R., & García, A. E. (2011). Influence of water–protein hydrogen bonding on the stability of Trp-cage miniprotein. A comparison between the TIP3P and TIP4P-Ew water models. Physical Chemistry Chemical Physics, 13(44), 19840–19847. https://doi.org/10.1039/C1CP22110H
- Petros, A. M., Olejniczak, E. T., & Fesik, S. W. (2004). Structural biology of the Bcl-2 family of proteins. Biochimica Et Biophysica Acta, 1644(2-3), 83–94. https://doi.org/10.1016/j.bbamcr.2003.08.012
- Pham, V.-C., Choi, M.-J., Kim, T.-W., Kim, J.-A., Choo, D.-J., Lee, K.-T., & Lee, J.-Y. (2012). CoMFA and CoMSIA studies on 1H-Furan-2, 5-dione and 1H-Pyrrole-2, 5-dione as PGE 2 production inhibitor. Bulletin of the Korean Chemical Society, 33(1), 305–308. https://doi.org/10.5012/bkcs.2012.33.1.305
- Placzek, W. J., Wei, J., Kitada, S., Zhai, D., Reed, J. C., & Pellecchia, M. (2010). A survey of the anti-apoptotic Bcl-2 subfamily expression in cancer types provides a platform to predict the efficacy of Bcl-2 antagonists in cancer therapy. Cell Death & Disease, 1(5), e40–e40. https://doi.org/10.1038/cddis.2010.18
- Qiu, J., Levin, L. R., Buck, J., & Reidenberg, M. M. (2002). Different pathways of cell killing by gossypol enantiomers. Experimental Biology and Medicine, 227(6), 398–401. https://doi.org/10.1177/153537020222700605
- Roy, K. (2007). On some aspects of validation of predictive quantitative structure–activity relationship models. Expert Opinion on Drug Discovery, 2(12), 1567–1577. https://doi.org/10.1517/17460441.2.12.1567
- Shaw, S., Bian, Z., Zhao, B., Tarr, J. C., Veerasamy, N., Jeon, K. O., Belmar, J., Arnold, A. L., Fogarty, S. A., & Perry, E. (2018). Optimization of potent and selective tricyclic indole diazepinone myeloid cell leukemia-1 inhibitors using structure-based design. Journal of Medicinal Chemistry, 61(6), 2410–2421. https://doi.org/10.1021/acs.jmedchem.7b01155
- Stewart, M. L., Fire, E., Keating, A. E., & Walensky, L. D. (2010). The MCL-1 BH3 helix is an exclusive MCL-1 inhibitor and apoptosis sensitizer. Nature Chemical Biology, 6(8), 595–601. https://doi.org/10.1038/nchembio.391
- Tabti, K., Baammi, S., ElMchichi, L., Sbai, A., Maghat, H., Bouachrine, M., & Lakhlifi, T. (2022). Computational investigation of pyrrolidin derivatives as novel GPX4/MDM2–p53 inhibitors using 2D/3D-QSAR, ADME/toxicity, molecular docking, molecular dynamics simulations, and MM-GBSA free energy. Structural Chemistry, 33(4), 1019–1039. https://doi.org/10.1007/s11224-022-01903-5
- Tabti, K., Elmchichi, L., Sbai, A., Maghat, H., Bouachrine, M., Lakhlifi, T., & Ghosh, A. (2022). 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, 132291. https://doi.org/10.1016/j.molstruc.2021.132291
- Tabti, K., Elmchichi, L., Sbai, A., Maghat, H., & Lakhlifi, T. (2022). HQSAR, CoMFA, CoMSIA docking studies and simulation MD on quinazolines/quinolines derivatives for DENV. Virus Inhibitory Activity, 5, 1937–1958. https://doi.org/10.1007/s42250-022-00484-4
- Touzeau, C., Dousset, C., Le Gouill, S., Sampath, D., Leverson, J. D., Souers, A. J., Maiga, S., Bene, M. C., Moreau, P., & Pellat-Deceunynck, C. (2014). The Bcl-2 specific BH3 mimetic ABT-199: A promising targeted therapy for t (11; 14) multiple myeloma. Leukemia, 28(1), 210–212. https://doi.org/10.1038/leu.2013.216
- Tripos International. (2012). Sybyl-X 2.0. Tripos International St. Louis.
- Tropsha, A., & Golbraikh, A. (2007). Predictive QSAR modeling workflow, model applicability domains, and virtual screening. Current Pharmaceutical Design, 13(34), 3494–3504. https://doi.org/10.2174/138161207782794257
- Umar, A. B., Uzairu, A., Shallangwa, G. A., & Uba, S. (2020). Computational evaluation of potent 2-(1H-imidazol-2-yl) pyridine derivatives as potential V600E-BRAF inhibitors. Egyptian Journal of Medical Human Genetics, 21(1), 1–11. https://doi.org/10.1186/s43042-020-00111-2
- Wang, L., Sloper, D. T., Addo, S. N., Tian, D., Slaton, J. W., & Xing, C. (2008). WL-276, an antagonist against Bcl-2 proteins, overcomes drug resistance and suppresses prostate tumor growth. Cancer Research, 68(11), 4377–4383. https://doi.org/10.1158/0008-5472.CAN-07-6590
- Wan, Y., Liu, T., Li, X., Chen, C., & Fang, H. (2017). Improved binding affinities of pyrrolidine derivatives as Mcl-1 inhibitors by modifying amino acid side chains. Bioorganic & Medicinal Chemistry, 25(1), 138–152. https://doi.org/10.1016/j.bmc.2016.10.020
- Wan, Y., Wang, J., Chen, M., Hou, X., & Fang, H. (2015). Design, synthesis and preliminary biological studies of pyrrolidine derivatives as Mcl-1 inhibitors. Bioorganic & Medicinal Chemistry, 23(24), 7685–7693. https://doi.org/10.1016/j.bmc.2015.11.014
- Wertz, I. E., Kusam, S., Lam, C., Okamoto, T., Sandoval, W., Anderson, D. J., Helgason, E., Ernst, J. A., Eby, M., Liu, J., Belmont, L. D., Kaminker, J. S., O'Rourke, K. M., Pujara, K., Kohli, P. B., Johnson, A. R., Chiu, M. L., Lill, J. R., Jackson, P. K., … Dixit, V. M. (2011). Sensitivity to antitubulin chemotherapeutics is regulated by MCL1 and FBW7. Nature, 471(7336), 110–114. https://doi.org/10.1038/nature09779
- Xing, C., Wang, L., Tang, X., & Sham, Y. Y. (2007). Development of selective inhibitors for anti-apoptotic Bcl-2 proteins from BHI-1. Bioorganic & Medicinal Chemistry, 15(5), 2167–2176. https://doi.org/10.1016/j.bmc.2006.12.020
- Yan, W., Lin, G., Zhang, R., Liang, Z., Wu, L., & Wu, W. (2020). Studies on molecular mechanism between ACE and inhibitory peptides in different bioactivities by 3D-QSAR and MD simulations. Journal of Molecular Liquids, 304, 112702. https://doi.org/10.1016/j.molliq.2020.112702
- Zack, T. I., Schumacher, S. E., Carter, S. L., Cherniack, A. D., Saksena, G., Tabak, B., Lawrence, M. S., Zhang, C.-Z., Wala, J., & Mermel, C. H. (2013). Pan-cancer patterns of somatic copy number alteration. Nature Genetics, 45(10), 1134–1140. https://doi.org/10.1038/ng.2760
- Zhang, H., Guttikonda, S., Roberts, L., Uziel, T., Semizarov, D., Elmore, S. W., Leverson, J. D., & Lam, L. T. (2011). Mcl-1 is critical for survival in a subgroup of non-small-cell lung cancer cell lines. Oncogene, 30(16), 1963–1968. https://doi.org/10.1038/onc.2010.559
- Zhou, P., Levy, N. B., Xie, H., Qian, L., Lee, C.-Y G., Gascoyne, R. D., & Craig, R. W. (2001). MCL1 transgenic mice exhibit a high incidence of B-cell lymphoma manifested as a spectrum of histologic subtypes. Blood, 97(12), 3902–3909. https://doi.org/10.1182/blood.V97.12.3902
- Zhou, W., Wang, Y., Lu, A., & Zhang, G. (2016). Systems pharmacology in small molecular drug discovery. International Journal of Molecular Sciences, 17(2), 246. https://doi.org/10.3390/ijms17020246