Multisampling-based docking reveals Imidazolidinyl urea as a multitargeted inhibitor for lung cancer: an optimisation followed multi-simulation and in-vitro study

References

• Abudayah, A., Daoud, S., Al‐Sha’er, M. A., & Omar Taha, M. (2022). Pharmacophore modeling of targets infested with activity cliffs via molecular dynamics simulation coupled with QSAR and comparison with other pharmacophore generation methods: KDR as case study. Molecular Informatics, 41(11), 2200049. https://doi.org/10.1002/minf.202200049
   Web of Science ®Google Scholar
• Adhikari, M., Dhaker, A., Adhikari, J., Ivanov, V., Singh, V., Chawla, R., Kumar, R., Sharma, R., Karamalakova, Y., Gadjeva, V., & Arora, R. (2013). In vitro studies on radioprotective efficacy of silymarin against gamma-irradiation. International Journal of Radiation Biology, 89(3), 200–211. https://doi.org/10.3109/09553002.2013.741285
   PubMed Web of Science ®Google Scholar
• Ahmad, S., Bano, N., Qazi, S., Yadav, M. K., Ahmad, N., & Raza, K. (2022). Multitargeted molecular dynamic understanding of butoxypheser against SARS-CoV-2: An in silico study. Natural Product Communications, 17(7), 1934578X2211154. https://doi.org/10.1177/1934578X221115499
   Web of Science ®Google Scholar
• Ahmad, S., Pasha Km, M., Raza, K., Rafeeq, M. M., Habib, A. H., Eswaran, M., & Yadav, M. K. (2022). Reporting dinaciclib and theodrenaline as a multitargeted inhibitor against SARS-CoV-2: An in-silico study. Journal of Biomolecular Structure and Dynamics, 1–11. https://doi.org/10.1080/07391102.2022.2060308
   Web of Science ®Google Scholar
• Alghamdi, Y. S., Mashraqi, M. M., Alzamami, A., Alturki, N. A., Ahmad, S., Alharthi, A. A., Alshamrani, S., & Asiri, S. A. (2022). Unveiling the multitargeted potential of N-(4-Aminobutanoyl)-S-(4-methoxybenzyl)-L-cysteinylglycine (NSL-CG) against SARS CoV-2: A virtual screening and molecular dynamics simulation study. Journal of Biomolecular Structure and Dynamics, 1–10. https://doi.org/10.1080/07391102.2022.2110158
   Web of Science ®Google Scholar
• Al-Sha’er, M. A., & Taha, M. O. (2021). Elaboration of novel TTK1 inhibitory leads via QSAR-guided selection of crystallographic pharmacophores followed by in vitro assay. Current Computer-Aided Drug Design, 17(4), 511–522. https://doi.org/10.2174/1573409916666200611122736
   PubMed Web of Science ®Google Scholar
• Al-Sha’er, M. A., Basheer, H. A., & Taha, M. O. (2023). Discovery of new PKN2 inhibitory chemotypes via QSAR-guided selection of docking-based pharmacophores. Molecular Diversity, 27(1), 443–462. https://doi.org/10.1007/s11030-022-10434-4
   PubMed Web of Science ®Google Scholar
• Alzamami, A., Alturki, N. A., Alghamdi, Y. S., Ahmad, S., Alshamrani, S., Asiri, S. A., & Mashraqi, M. M. (2022). Hemi-Babim and fenoterol as potential inhibitors of MPro and papain-like protease against SARS-CoV-2: An in-silico study. Medicina, 58(4), 515. https://doi.org/10.3390/medicina58040515
   PubMedGoogle Scholar
• Ayyagari Ramlal, Shaban Ahmad, Laxman Kumar, Fatima Nazish Khan, Rubina Chongtham. (2021). From molecules to patients: The clinical applications of biological databases and electronic health records, in Translational bioinformatics in healthcare and medicine (pp. 107–125). Academic Press.
   Google Scholar
• Brown, J. M., & Attardi, L. D. (2005). The role of apoptosis in cancer development and treatment response. Nature Reviews. Cancer, 5(3), 231–237. https://doi.org/10.1038/nrc1560
   PubMed Web of Science ®Google Scholar
• Chrysostomou, S., Roy, R., Prischi, F., Thamlikitkul, L., Chapman, K. L., Mufti, U., Peach, R., Ding, L., Hancock, D., Moore, C., Molina-Arcas, M., Mauri, F., Pinato, D. J., Abrahams, J. M., Ottaviani, S., Castellano, L., Giamas, G., Pascoe, J., Moonamale, D., … Pardo, O. E. (2021). Repurposed floxacins targeting RSK4 prevent chemoresistance and metastasis in lung and bladder cancer. Science Translational Medicine, 13(602), eaba4627. https://doi.org/10.1126/scitranslmed.aba4627
   PubMed Web of Science ®Google Scholar
• Clarke, P. G., & Clarke, S. (1996). Nineteenth century research on naturally occurring cell death and related phenomena. Anatomy and Embryology, 193(2), 81–99. https://doi.org/10.1007/BF00214700
   PubMedGoogle Scholar
• Corrales, L., Rosell, R., Cardona, A. F., Martín, C., Zatarain-Barrón, Z. L., & Arrieta, O. (2020). Lung cancer in never smokers: The role of different risk factors other than tobacco smoking. Critical Reviews in Oncology/Hematology, 148, 102895. https://doi.org/10.1016/j.critrevonc.2020.102895
   PubMed Web of Science ®Google Scholar
• Eck, M. J., & Sprang, S. R. (1989). The structure of tumor necrosis factor-α at 2.6 Å resolution: Implications for receptor binding. The Journal of Biological Chemistry, 264(29), 17595–17605. https://doi.org/10.1016/S0021-9258(18)71533-0
   PubMed Web of Science ®Google Scholar
• El-Baz, A., Beache, G. M., Gimel’farb, G., Suzuki, K., Okada, K., Elnakib, A., Soliman, A., & Abdollahi, B. (2013). Computer-aided diagnosis systems for lung cancer: Challenges and methodologies. International Journal of Biomedical Imaging, 2013, 1–46. https://doi.org/10.1155/2013/942353
   Google Scholar
• Ferreira, L. L., & Andricopulo, A. D. (2019). ADMET modeling approaches in drug discovery. Drug Discovery Today, 24(5), 1157–1165. https://doi.org/10.1016/j.drudis.2019.03.015
   PubMed Web of Science ®Google Scholar
• Fink, S. L., & Cookson, B. T. (2005). Apoptosis, pyroptosis, and necrosis: Mechanistic description of dead and dying eukaryotic cells. Infection and Immunity, 73(4), 1907–1916. https://doi.org/10.1128/IAI.73.4.1907-1916.2005
   PubMed Web of Science ®Google Scholar
• Forte, G. C., Altmayer, S., Silva, R. F., Stefani, M. T., Libermann, L. L., Cavion, C. C., Youssef, A., Forghani, R., King, J., Mohamed, T.-L., Andrade, R. G. F., & Hochhegger, B. (2022). Deep learning algorithms for diagnosis of lung cancer: A systematic review and meta-analysis. Cancers, 14(16), 3856. https://doi.org/10.3390/cancers14163856
   PubMed Web of Science ®Google Scholar
• Gupta, D., Crosby, M. E., Almasan, A., & Macklis, R. M. (2008). Regulation of CD20 expression by radiation-induced changes in intracellular redox status. Free Radical Biology & Medicine, 44(4), 614–623. https://doi.org/10.1016/j.freeradbiomed.2007.10.048
   PubMed Web of Science ®Google Scholar
• Hansson, T., Oostenbrink, C., & van Gunsteren, W. (2002). Molecular dynamics simulations. Current Opinion in Structural Biology, 12(2), 190–196. https://doi.org/10.1016/s0959-440x(02)00308-1
   PubMed Web of Science ®Google Scholar
• Karch, J., & Molkentin, J. D. (2015). Regulated necrotic cell death. Circulation Research, 116(11), 1800–1809. https://doi.org/10.1161/CIRCRESAHA.116.305421
   PubMed Web of Science ®Google Scholar
• Karplus, M., & Petsko, G. A. (1990). Molecular dynamics simulations in biology. Nature, 347(6294), 631–639. https://doi.org/10.1038/347631a0
   PubMed Web of Science ®Google Scholar
• Kenfield, S. A., Wei, E. K., Stampfer, M. J., Rosner, B. A., & Colditz, G. A. (2008). Comparison of aspects of smoking among the four histological types of lung cancer. Tobacco Control, 17(3), 198–204. https://doi.org/10.1136/tc.2007.022582
   PubMed Web of Science ®Google Scholar
• Khan, N., Shah, P. P., Ban, D., Trigo-Mouriño, P., Carneiro, M. G., DeLeeuw, L., Dean, W. L., Trent, J. O., Beverly, L. J., Konrad, M., Lee, D., & Sabo, T. M. (2019). Solution structure and functional investigation of human guanylate kinase reveals allosteric networking and a crucial role for the enzyme in cancer. The Journal of Biological Chemistry, 294(31), 11920–11933. https://doi.org/10.1074/jbc.RA119.009251
   PubMed Web of Science ®Google Scholar
• Lauren G Collins, Christopher Haines, Robert Perkel, Robert E Enck. (2007). Lung cancer: Diagnosis and management. American Family Physician, 75(1), 56–63.
   PubMed Web of Science ®Google Scholar
• Lawrie, A. M., Noble, M. E., Tunnah, P., Brown, N. R., Johnson, L. N., & Endicott, J. A. (1997). Protein kinase inhibition by staurosporine revealed in details of the molecular interaction with CDK2. Nature Structural Biology, 4(10), 796–801. https://doi.org/10.1038/nsb1097-796
   PubMedGoogle Scholar
• Lin, J. J., & Shaw, A. T. (2016). Resisting resistance: Targeted therapies in lung cancer. Trends in Cancer, 2(7), 350–364. https://doi.org/10.1016/j.trecan.2016.05.010
   PubMed Web of Science ®Google Scholar
• Lu, C., Wu, C., Ghoreishi, D., Chen, W., Wang, L., Damm, W., Ross, G. A., Dahlgren, M. K., Russell, E., Von Bargen, C. D., Abel, R., Friesner, R. A., & Harder, E. D. (2021). OPLS4: Improving force field accuracy on challenging regimes of chemical space. Journal of Chemical Theory and Computation, 17(7), 4291–4300. https://doi.org/10.1021/acs.jctc.1c00302
   PubMed Web of Science ®Google Scholar
• Lundov, M. D., Moesby, L., Zachariae, C., & Johansen, J. D. (2009). Contamination versus preservation of cosmetics: A review on legislation, usage, infections, and contact allergy. Contact Dermatitis, 60(2), 70–78. https://doi.org/10.1111/j.1600-0536.2008.01501.x
   PubMed Web of Science ®Google Scholar
• Majno, G., & Joris, I. (1995). Apoptosis, oncosis, and necrosis. An overview of cell death. The American Journal of Pathology, 146(1), 3–15.
   PubMed Web of Science ®Google Scholar
• Maurício, E., Rosado, C., Duarte, M., Verissimo, J., Bom, S., & Vasconcelos, L. (2017). Efficiency of nisin as preservative in cosmetics and topical products. Cosmetics, 4(4), 41. https://doi.org/10.3390/cosmetics4040041
   Google Scholar
• McDonald, I. (1972). NpT-ensemble Monte Carlo calculations for binary liquid mixtures. Molecular Physics, 23(1), 41–58. https://doi.org/10.1080/00268977200100031
   Web of Science ®Google Scholar
• Niefind, K., Guerra, B., Ermakowa, I., & Issinger, O. G. (2001). Crystal structure of human protein kinase CK2: Insights into basic properties of the CK2 holoenzyme. The EMBO Journal, 20(19), 5320–5331. https://doi.org/10.1093/emboj/20.19.5320
   PubMed Web of Science ®Google Scholar
• Norinder, U., & Bergström, C. A. (2006). Prediction of ADMET properties. ChemMedChem, 1(9), 920–937. https://doi.org/10.1002/cmdc.200600155
   PubMed Web of Science ®Google Scholar
• O’Keeffe, L. M., Taylor, G., Huxley, R. R., Mitchell, P., Woodward, M., & Peters, S. A. E. (2018). Smoking as a risk factor for lung cancer in women and men: A systematic review and meta-analysis. BMJ Open, 8(10), e021611. https://doi.org/10.1136/bmjopen-2018-021611
   PubMed Web of Science ®Google Scholar
• Oronsky, B., Abrouk, N., Caroen, S., Lybeck, M., Guo, X., Wang, X., Yu, Z., & Reid, T. (2022). A 2022 update on extensive stage small-cell lung cancer (SCLC). Journal of Cancer, 13(9), 2945–2953. https://doi.org/10.7150/jca.75622
   PubMed Web of Science ®Google Scholar
• Owen, J. R., Nabney, I. T., Medina-Franco, J. L., & López-Vallejo, F. (2011). Visualization of molecular fingerprints. Journal of Chemical Information and Modeling, 51(7), 1552–1563. https://doi.org/10.1021/ci1004042
   PubMed Web of Science ®Google Scholar
• Ramesh, R. (2010). Drug resistance in lung cancer. Lung Cancer: Targets and Therapy, 1, 23. https://doi.org/10.2147/LCTT.S6861
   PubMedGoogle Scholar
• Rapaport, D. C. (2004). The art of molecular dynamics simulation. Cambridge University Press.
   Google Scholar
• Ricci, M. S., & Zong, W. X. (2006). Chemotherapeutic approaches for targeting cell death pathways. The Oncologist, 11(4), 342–357. https://doi.org/10.1634/theoncologist.11-4-342
   PubMed Web of Science ®Google Scholar
• Rose, P. W., Beran, B., Bi, C., Bluhm, W. F., Dimitropoulos, D., Goodsell, D. S., Prlic, A., Quesada, M., Quinn, G. B., Westbrook, J. D., Young, J., Yukich, B., Zardecki, C., Berman, H. M., & Bourne, P. E. (2011). The RCSB Protein Data Bank: Redesigned web site and web services. Nucleic Acids Research, 39(Database issue), D392–D401. https://doi.org/10.1093/nar/gkq1021
   PubMedGoogle Scholar
• Saraste, A., & Pulkki, K. (2000). Morphologic and biochemical hallmarks of apoptosis. Cardiovascular Research, 45(3), 528–537. https://doi.org/10.1016/s0008-6363(99)00384-3
   PubMed Web of Science ®Google Scholar
• Schabath, M. B., & Cote, M. L. (2019). Cancer progress and priorities: Lung cancer. Cancer Epidemiology, Biomarkers & Prevention: A Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology, 28(10), 1563–1579. https://doi.org/10.1158/1055-9965.EPI-19-0221
   PubMed Web of Science ®Google Scholar
• Schrödinger LLC. (2015). Jaguar. Schrödinger release 4. Available from https://www.schrodinger.com/
   Google Scholar
• Schrödinger LLC. (2015). Maestro. Schrödinger Release, 2, 2015.
   Google Scholar
• Schrödinger Release. (2016). 4: Protein preparation wizard (pp. 2018–2013). Epik, Schrödinger, LLC.
   Google Scholar
• Schrödinger Release. (2017). 1: Maestro. Schrödinger, LLC.
   Google Scholar
• Schrödinger Release. (2017). 2: LigPrep. Schrödinger, LLC. New York, NY, 2017.
   Google Scholar
• Schrödinger Release. (2017). 3: Desmond molecular dynamics system, DE Shaw research, Maestro-Desmond Interoperability Tools. Schrödinger.
   Google Scholar
• Schrödinger Release. (2017). 4: Desmond molecular dynamics system. DE Shaw Research.
   Google Scholar
• Schrödinger Release. (2018). 4: Glide. Schrödinger, LLC. 757.
   Google Scholar
• Schrödinger Release. (2020). 1: Epik.(2020). Schrödinger Release, 1. Schrödinger, LLC.
   Google Scholar
• Schrödinger Release. (2020). 1: Prime. Schrödinger, LLC.
   Google Scholar
• Schrödinger Release. (2020). 1: QikProp. Schrödinger, LLC. 329.
   Google Scholar
• Singh, V., Gupta, D., Arora, R., Tripathi, R. P., Almasan, A., & Macklis, R. M. (2014). Surface levels of CD20 determine anti-CD20 antibodies mediated cell death in vitro. PLoS One, 9(11), e111113. https://doi.org/10.1371/journal.pone.0111113
   PubMed Web of Science ®Google Scholar
• Vargas, A. J., & Harris, C. C. (2016). Biomarker development in the precision medicine era: Lung cancer as a case study. Nature Reviews. Cancer, 16(8), 525–537. https://doi.org/10.1038/nrc.2016.56
   PubMed Web of Science ®Google Scholar
• Wirsdörfer, F., De Leve, S., & Jendrossek, V. (2018). Combining radiotherapy and immunotherapy in lung cancer: Can we expect limitations due to altered normal tissue toxicity? International Journal of Molecular Sciences, 20(1), 24. https://doi.org/10.3390/ijms20010024
   PubMed Web of Science ®Google Scholar
• Wishart, D. S., Feunang, Y. D., Guo, A. C., Lo, E. J., Marcu, A., Grant, J. R., Sajed, T., Johnson, D., Li, C., Sayeeda, Z., Assempour, N., Iynkkaran, I., Liu, Y., Maciejewski, A., Gale, N., Wilson, A., Chin, L., Cummings, R., Le, D., … Wilson, M. (2018). DrugBank 5.0: A major update to the DrugBank database for 2018. Nucleic Acids Research, 46(D1), D1074–D1082. https://doi.org/10.1093/nar/gkx1037
   PubMed Web of Science ®Google Scholar
• Ziegler, U., & Groscurth, P. (2004). Morphological features of cell death. News in Physiological Sciences: An International Journal of Physiology Produced Jointly by the International Union of Physiological Sciences and the American Physiological Society, 19, 124–128. https://doi.org/10.1152/nips.01519.2004
   PubMedGoogle Scholar