130
Views
0
CrossRef citations to date
0
Altmetric
Research Article

Variolin B from sea sponge against lung cancer: a multitargeted molecular docking with fingerprinting and molecular dynamics simulation study

, ORCID Icon, ORCID Icon, ORCID Icon, &
Pages 3507-3519 | Received 08 Feb 2023, Accepted 07 May 2023, Published online: 19 Oct 2023

References

  • Achonu, C. U., Iwuchukwu, P. J., & Ogunleye, E. (2022). Case study on small lung cell carcinoma in A 26-year-old male. American Journal of Health, Medicine and Nursing Practice, 7(2), 15–23. https://doi.org/10.47672/ajhmn.912
  • Ahmad, S., & Raza, K. (2023). Identification of 5-nitroindazole as a multitargeted inhibitor for CDK and transferase kinase in lung cancer: A multisampling algorithm-based structural study. Molecular Diversity, 2023, 1–14. https://doi.org/10.1007/s11030-023-10648-0
  • 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
  • Ahmad, S., Bhanu, P., Kumar, J., Pathak, R. K., Mallick, D., Uttarkar, A., Niranjan, V., & Mishra, V. (2022). Molecular dynamics simulation and docking analysis of NF-κB protein binding with sulindac acid. Bioinformation, 18(3), 170–179. https://doi.org/10.6026/97320630018170
  • Ahmad, S., et al. (2021). Mobile technology solution for COVID-19: Surveillance and prevention. In Computational intelligence methods in COVID-19: Surveillance, prevention, prediction and diagnosis (pp. 79–108). Springer.
  • Ahmad, S., Pasha Km, M., Raza, K., Rafeeq, M. M., Habib, A. H., Eswaran, M., & Yadav, M. K. (2023). Reporting dinaciclib and theodrenaline as a multitargeted inhibitor against SARS-CoV-2: An in-silico study. Journal of Biomolecular Structure & Dynamics, 41(9), 4013–4023. https://doi.org/10.1080/07391102.2022.2060308
  • Ahmad, S., Sayeed, S., Bano, N., Sheikh, K., & Raza, K. (2022). In-silico analysis reveals Quinic acid as a multitargeted inhibitor against cervical cancer. Journal of Biomolecular Structure & Dynamics, 2022, 1–17. https://doi.org/10.1080/07391102.2022.2146202
  • Ahmad, S., Singh, V., Gautam, H. K., & Raza, K. (2023). Multisampling-based docking reveals Imidazolidinyl urea as a multitargeted inhibitor for Lung Cancer: An optimisation followed multi-simulation and in-vitro study. Journal of Biomolecular Structure & Dynamics, 2023, 1–18. https://doi.org/10.1080/07391102.2023.2209673
  • Alghamdi, Y. S., Mashraqi, M. M., Alzamami, A., Alturki, N. A., Ahmad, S., Alharthi, A. A., Alshamrani, S., & Asiri, S. A. (2023). 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 & Dynamics, 41(14), 6633–6642. https://doi.org/10.1080/07391102.2022.2110158
  • Alturki, N. A., Mashraqi, M. M., Alzamami, A., Alghamdi, Y. S., Alharthi, A. A., Asiri, S. A., Ahmad, S., & Alshamrani, S. (2022). In-silico screening and molecular dynamics simulation of drug bank experimental compounds against SARS-CoV-2. Molecules, 27(14), 4391. https://doi.org/10.3390/molecules27144391
  • 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
  • Attwood, M. M., Fabbro, D., Sokolov, A. V., Knapp, S., & Schiöth, H. B. (2021). Trends in kinase drug discovery: Targets, indications and inhibitor design. Nature Reviews. Drug Discovery, 20(11), 839–861. https://doi.org/10.1038/s41573-021-00252-y
  • Barh, D., Tiwari, S., Rodrigues Gomes, L. G., Ramalho Pinto, C. H., Andrade, B. S., Ahmad, S., Aljabali, A. A. A., Alzahrani, K. J., Banjer, H. J., Hassan, S. S., Redwan, E. M., Raza, K., Góes-Neto, A., Sabino-Silva, R., Lundstrom, K., Uversky, V. N., Azevedo, V., & Tambuwala, M. M. (2023). SARS-CoV-2 variants show a gradual declining pathogenicity and pro-inflammatory cytokine stimulation, an increasing antigenic and anti-inflammatory cytokine induction, and rising structural protein instability: A minimal number genome-based approach. Inflammation, 46(1), 297–312. https://doi.org/10.1007/s10753-022-01734-w
  • Behera, D., & Balamugesh, T. (2004). Lung cancer in India. Indian J Chest Dis Allied Science, 46, 269.
  • Boko, K. (2022). Disease free interval and survival analysis after surgical treatment in patients with non-small-cell lung cancer. University of Split. School of Medicine.
  • Borgo, C., & Ruzzene, M. (2019). Role of protein kinase CK2 in antitumor drug resistance. Journal of Experimental & Clinical Cancer Research, 38(1), 1–15. https://doi.org/10.1186/s13046-019-1292-y
  • Canals, A., Arribas-Bosacoma, R., Albericio, F., Álvarez, M., Aymamí, J., & Coll, M. (2017). Intercalative DNA binding of the marine anticancer drug variolin B. Scientific Reports, 7(1), 39680. https://doi.org/10.1038/srep39680
  • Cappel, D., Sherman, W., & Beuming, T. (2017). Calculating water thermodynamics in the binding site of proteins–applications of WaterMap to drug discovery. Current Topics in Medicinal Chemistry, 17(23), 2586–2598. https://doi.org/10.2174/1568026617666170414141452
  • Chaouachi, K. (2009). Hookah (shisha, narghile) smoking and environmental tobacco smoke (ETS). A critical review of the relevant literature and the public health consequences. International Journal of Environmental Research and Public Health, 6(2), 798–843. https://doi.org/10.3390/ijerph6020798
  • 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
  • Deo, S., Sharma, J., & Kumar, S. (2022). GLOBOCAN 2020 report on global cancer burden: Challenges and opportunities for surgical oncologists. Annals of Surgical Oncology, 29(11), 6497–6500. https://doi.org/10.1245/s10434-022-12151-6
  • 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
  • Famuyiwa, S. O., Ahmad, S., Fakola, E. G., Olusola, A. J., Adesida, S. A., Obagunle, F. O., Raza, K., Ugwo, J. P., Oyelekan, E. I., & Faloye, K. O. (2023). Comprehensive computational studies of naturally occurring kuguacins as antidiabetic agents by targeting visfatin. Chemistry Africa, 6(3), 1415–1427. https://doi.org/10.1007/s42250-023-00604-8
  • Florea, A.-M., & Büsselberg, D. (2011). Cisplatin as an anti-tumor drug: Cellular mechanisms of activity, drug resistance and induced side effects. Cancers, 3(1), 1351–1371. https://doi.org/10.3390/cancers3011351
  • Gangwar, S. K., Kumar, A., Yap, K. C.-H., Jose, S., Parama, D., Sethi, G., Kumar, A. P., & Kunnumakkara, A. B. (2022). Targeting nuclear receptors in lung cancer – Novel therapeutic prospects. Pharmaceuticals, 15(5), 624. https://doi.org/10.3390/ph15050624
  • Gristina, V., Cupri, M. G., Torchio, M., Mezzogori, C., Cacciabue, L., & Danova, M. (2015). Diabetes and cancer: A critical appraisal of the pathogenetic and therapeutic links. Biomedical Reports, 3(2), 131–136. https://doi.org/10.3892/br.2014.399
  • Hanif, I. M., Hanif, I. M., Shazib, M. A., Ahmad, K. A., & Pervaiz, S. (2010). Casein Kinase II: An attractive target for anti-cancer drug design. The International Journal of Biochemistry & Cell Biology, 42(10), 1602–1605. https://doi.org/10.1016/j.biocel.2010.06.010
  • Hong, H., & Benveniste, E. N. (2021). The immune regulatory role of protein kinase CK2 and its implications for treatment of cancer. Biomedicines, 9(12), 1932. https://doi.org/10.3390/biomedicines9121932
  • Joly, A.-L., Wettstein, G., Mignot, G., Ghiringhelli, F., & Garrido, C. (2010). Dual role of heat shock proteins as regulators of apoptosis and innate immunity. Journal of Innate Immunity, 2(3), 238–247. https://doi.org/10.1159/000296508
  • Karwasra, R., Ahmad, S., Bano, N., Qazi, S., Raza, K., Singh, S., & Varma, S. (2022). Macrophage-targeted punicalagin nanoengineering to alleviate Methotrexate-Induced Neutropenia: A molecular docking, DFT, and MD simulation analysis. Molecules, 27(18), 6034. https://doi.org/10.3390/molecules27186034
  • Karwasra, R., Khanna, K., Singh, S., Ahmad, S., & Verma, S. (2022). The incipient role of computational intelligence in oncology: Drug designing, discovery, and development (pp. 369–384). In Computational intelligence in oncology. Springer. https://doi.org/10.1007/978-981-16-9221-5_21
  • Kaul, T., Eswaran, M., Ahmad, S., Thangaraj, A., Jain, R., Kaul, R., Raman, N. M., & Bharti, J. (2020). Probing the effect of a plus 1bp frameshift mutation in protein-DNA interface of domestication gene, NAMB1, in wheat. Journal of Biomolecular Structure & Dynamics, 38(12), 3633–3647. https://doi.org/10.1080/07391102.2019.1680435
  • 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
  • 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
  • Liang, S., Zhou, G., & Hu, W. (2022). Research progress of heavy ion radiotherapy for non-small-cell lung cancer. International Journal of Molecular Sciences, 23(4), 2316. https://doi.org/10.3390/ijms23042316
  • Lianos, G. D., Alexiou, G. A., Mangano, A., Mangano, A., Rausei, S., Boni, L., Dionigi, G., & Roukos, D. H. (2015). The role of heat shock proteins in cancer. Cancer Letters, 360(2), 114–118. https://doi.org/10.1016/j.canlet.2015.02.026
  • 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
  • Mathur, P., Sathishkumar, K., Chaturvedi, M., Das, P., Sudarshan, K. L., Santhappan, S., Nallasamy, V., John, A., Narasimhan, S., Roselind, F. S., on behalf of ICMR-NCDIR-NCRP Investigator Group. (2020). Cancer statistics, 2020: Report from national cancer registry programme, India. Journal of Clinical Oncology – Global Oncology, 6, 1063–1075.
  • McCracken, M., Olsen, M., Chen, M. S., Jemal, A., Thun, M., Cokkinides, V., Deapen, D., & Ward, E. (2007). Cancer incidence, mortality, and associated risk factors among Asian Americans of Chinese, Filipino, Vietnamese, Korean, and Japanese ethnicities. A Cancer Journal for Clinicians, 57(4), 190–205. https://doi.org/10.3322/canjclin.57.4.190
  • Padhiary, S., Samal, D., Khandayataray, P., & Murthy, M. K. (2021). A systematic review report on tobacco products and its health issues in India. Reviews on Environmental Health, 36(3), 367–389. https://doi.org/10.1515/reveh-2020-0037
  • QikProp. (2017). Schrödinger Release 2017-1: QikProp. Schrödinger, LLC.
  • Rahman, M., & Fukui, T. (2000). Bidi smoking and health. Public Health, 114(2), 123–127. https://doi.org/10.1016/S0033-3506(00)00320-6
  • Ramlal, A., Ahmad, S., Kumar, L., Khan, F. N., & Chongtham, R. (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. https://doi.org/10.1016/B978-0-323-89824-9.00009-4
  • Release, S. (2017a). 2: LigPrep., New York, NY, 2017. Schrödinger, LLC.
  • Release, S. (2017b). 3: Desmond molecular dynamics system, DE Shaw research, New York, NY, 2017. Maestro-Desmond Interoperability Tools, Schrödinger.
  • Release, S. (2017c). 4: Desmond molecular dynamics system. DE Shaw Research.
  • Release, S. (2017d). 4: Maestro, Schrödinger, LLC, New York, NY, 2017. Google Scholar There is no corresponding record for this reference.
  • Release, S. (2017e). 4: Schrödinger Suite 2017-4 Protein Preparation Wizard; Epik, Schrödinger, LLC, New York, NY, 2017. Impact, Schrödinger, LLC.
  • Release, S. (2018). 4: Glide, 757. Schrödinger, LLC.
  • Release, S. (2020). 1: WaterMap. Schrödinger, LLC.
  • Schrödinger, L. (2011). Protein preparation wizard. Epik version 2.
  • Sheikh, K., Sayeed, S., Asif, A., Siddiqui, M. F., Rafeeq, M. M., Sahu, A., & Ahmad, S. (2023). Consequential innovations in nature-inspired intelligent computing techniques for biomarkers and potential therapeutics identification. In Nature-inspired intelligent computing techniques in bioinformatics (pp. 247–274). Springer. https://doi.org/10.1007/978-981-19-6379-7_13
  • Simone, M., Erba, E., Damia, G., Vikhanskaya, F., Di Francesco, A. M., Riccardi, R., Bailly, C., Cuevas, C., Fernandez Sousa-Faro, J. M., & D'Incalci, M. (2005). Variolin B and its derivate deoxy-variolin B: New marine natural compounds with cyclin-dependent kinase inhibitor activity. European Journal of Cancer, 41(15), 2366–2377. https://doi.org/10.1016/j.ejca.2005.05.015
  • Tarique, M., Ahmad, S., Malik, A., Ahmad, I., Saeed, M., Almatroudi, A., Qadah, T., Murad, M. A., Mashraqi, M., Alam, Q., & Al-Saleh, Y. (2021). Novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) and other coronaviruses: A genome-wide comparative annotation and analysis. Molecular and Cellular Biochemistry, 476(5), 2203–2217. https://doi.org/10.1007/s11010-020-04027-8
  • Torre, L. A., Sauer, A. M. G., Chen Jr, M. S., Kagawa‐Singer, M., Jemal, A., & Siegel, R. L. (2016). Cancer statistics for Asian Americans, Native Hawaiians, and Pacific Islanders, 2016: Converging incidence in males and females. A Cancer Journal for Clinicians, 66(3), 182–202. https://doi.org/10.3322/caac.21335
  • Tripathi, M. K., Ahmad, S., Tyagi, R., Dahiya, V., & Yadav, M. K. (2022). Fundamentals of molecular modeling in drug design. In Computer Aided Drug Design (CADD): From ligand-based methods to structure-based approaches (pp. 125–155). Elsevier. https://doi.org/10.1016/B978-0-323-90608-1.00001-0
  • Van Meerbeeck, J. P., Fennell, D. A., & De Ruysscher, D. K. (2011). Small-cell lung cancer. Lancet, 378(9804), 1741–1755. https://doi.org/10.1016/S0140-6736(11)60165-7
  • 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
  • Wishart, D. S., Knox, C., Guo, A. C., Cheng, D., Shrivastava, S., Tzur, D., Gautam, B., & Hassanali, M. (2008). DrugBank: A knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Research, 36(Database issue), D901–D906. https://doi.org/10.1093/nar/gkm958
  • Xia, C., Dong, X., Li, H., Cao, M., Sun, D., He, S., Yang, F., Yan, X., Zhang, S., Li, N., & Chen, W. (2022). Cancer statistics in China and United States, 2022: Profiles, trends, and determinants. Chinese Medical Journal, 135(5), 584–590. https://doi.org/10.1097/CM9.0000000000002108
  • Yadav, K., Upadhyay, S., Chandra, A., Hariprasad, R., Gupta, R., Mehrotra, R., Singh, S., & Gupta, S. (2020). Evaluation of ‘India against Cancer’web portal using environmental scan and Google Analytics. International Journal of Scientific Research in Network Security and Communication, 8, 1.
  • Yadav, M. K., Ahmad, S., Raza, K., Kumar, S., Eswaran, M., & Pasha Km, M. (2023). Predictive modeling and therapeutic repurposing of natural compounds against the receptor-binding domain of SARS-CoV-2. Journal of Biomolecular Structure & Dynamics, 41(5), 1527–1539. https://doi.org/10.1080/07391102.2021.2021993
  • Zhang, M.-Q., & Wilkinson, B. (2007). Drug discovery beyond the ‘rule-of-five’. Current Opinion in Biotechnology, 18(6), 478–488. https://doi.org/10.1016/j.copbio.2007.10.005

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.