A virtual screening investigation to identify bioactive natural compounds as potential inhibitors of cyclin-dependent kinase 9

References

• Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1–2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
   Google Scholar
• Ali, S., Khan, F. I., Mohammad, T., Lan, D., Hassan, M., & Wang, Y. (2019). Identification and evaluation of inhibitors of lipase from Malassezia restricta using virtual high-throughput screening and molecular dynamics studies. International Journal of Molecular Sciences, 20(4), 884. https://doi.org/10.3390/ijms20040884
   PubMed Web of Science ®Google Scholar
• Altis, A., Otten, M., Nguyen, P. H., Hegger, R., & Stock, G. (2008). Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis. The Journal of Chemical Physics, 128(24), 245102. https://doi.org/10.1063/1.2945165
   PubMed Web of Science ®Google Scholar
• Amadei, A., Linssen, A. B., & Berendsen, H. J. (1993). Essential dynamics of proteins. Proteins: Structure, Function, and Genetics, 17(4), 412–425. https://doi.org/10.1002/prot.340170408
   PubMed Web of Science ®Google Scholar
• Amir, M., Mohammad, T., Prasad, K., Hasan, G. M., Kumar, V., Dohare, R., Islam, A., Ahmad, F., & Imtaiyaz Hassan, M. (2020). Virtual high-throughput screening of natural compounds in-search of potential inhibitors for protection of telomeres 1 (POT1). Journal of Biomolecular Structure & Dynamics, 38(15), 4625–4634. https://doi.org/10.1080/07391102.2019.1682052
   PubMed Web of Science ®Google Scholar
• Anjum, F., Ali, F., Mohammad, T., Shafie, A., Akhtar, O., Abdullaev, B., & Hassan, I. (2021). Discovery of natural compounds as potential inhibitors of human carbonic anhydrase II: An integrated virtual screening, docking, and molecular dynamics simulation study. Omics : a Journal of Integrative Biology, 25(8), 513–524. https://doi.org/10.1089/omi.2021.0059
   PubMed Web of Science ®Google Scholar
• Anjum, F., Mohammad, T., Almalki, A. A., Akhtar, O., Abdullaev, B., & Hassan, M. I. (2021). Phytoconstituents and medicinal plants for anticancer drug discovery: Computational identification of potent inhibitors of PIM1 kinase. Omics : a Journal of Integrative Biology, 25(9), 580–590. https://doi.org/10.1089/omi.2021.0107
   PubMed Web of Science ®Google Scholar
• Anshabo, A. T., Milne, R., Wang, S., & Albrecht, H. (2021). CDK9: A comprehensive review of its biology, and its role as a potential target for anticancer agents. Frontiers in Oncology, 11, 1573. https://doi.org/10.3389/fonc.2021.678559
   Web of Science ®Google Scholar
• Baell, J. B. (2016). Feeling nature’s PAINS: Natural products, natural product drugs, and pan assay interference compounds (PAINS). Journal of Natural Products, 79(3), 616–628. https://doi.org/10.1021/acs.jnatprod.5b00947
   PubMed Web of Science ®Google Scholar
• Barboric, M., Nissen, R. M., Kanazawa, S., Jabrane-Ferrat, N., & Peterlin, B. M. (2001). NF-κB binds P-TEFb to stimulate transcriptional elongation by RNA polymerase II. Molecular Cell, 8(2), 327–337. https://doi.org/10.1016/s1097-2765(01)00314-8
   PubMed Web of Science ®Google Scholar
• Barlaam, B., Casella, R., Cidado, J., Cook, C., De Savi, C., Dishington, A., Donald, C. S., Drew, L., Ferguson, A. D., Ferguson, D., Glossop, S., Grebe, T., Gu, C., Hande, S., Hawkins, J., Hird, A. W., Holmes, J., Horstick, J., Jiang, Y., … Yao, T. (2020). Discovery of AZD4573, a potent and selective inhibitor of CDK9 that enables short duration of target engagement for the treatment of hematological malignancies. Journal of Medicinal Chemistry, 63(24), 15564–15590. https://doi.org/10.1021/acs.jmedchem.0c01754
   PubMed Web of Science ®Google Scholar
• Batool, M., Ahmad, B., & Choi, S. (2019). A structure-based drug discovery paradigm. International Journal of Molecular Sciences, 20(11), 2783. https://doi.org/10.3390/ijms20112783
   PubMed Web of Science ®Google Scholar
• Baumli, S., Lolli, G., Lowe, E. D., Troiani, S., Rusconi, L., Bullock, A. N., Debreczeni, J. É., Knapp, S., & Johnson, L. N. (2008). The structure of P‐TEFb (CDK9/cyclin T1), its complex with flavopiridol and regulation by phosphorylation. The EMBO Journal, 27(13), 1907–1918. https://doi.org/10.1038/emboj.2008.121
   PubMed Web of Science ®Google Scholar
• da Silva Rocha, S. F., Olanda, C. G., Fokoue, H. H., & Sant’Anna, C. M. (2019). Virtual screening techniques in drug discovery: Review and recent applications. Current Topics in Medicinal Chemistry, 19(19), 1751–1767. https://doi.org/10.2174/1568026619666190816101948
   PubMed Web of Science ®Google Scholar
• DeLano, W. L. (2002). Pymol: An open-source molecular graphics tool. CCP4 Newsletter on Protein Crystallography, 40, 82–92.
   Google Scholar
• Deng, Y., & Roux, B. (2009). Computations of standard binding free energies with molecular dynamics simulations. The Journal of Physical Chemistry. B, 113(8), 2234–2246. https://doi.org/10.1021/jp807701h
   PubMed Web of Science ®Google Scholar
• Eswar, N., Eramian, D., Webb, B., Shen, M.-Y., & Sali, A. (2008). Protein structure modeling with MODELLER. In Structural proteomics (pp. 145–159). Springer.
   Google Scholar
• Fatima, S., Mohammad, T., Jairajpuri, D. S., Rehman, M. T., Hussain, A., Samim, M., Ahmad, F. J., Alajmi, M. F., & Hassan, M. I. (2020). Identification and evaluation of glutathione conjugate gamma-l-glutamyl-l-cysteine for improved drug delivery to the brain. Journal of Biomolecular Structure & Dynamics, 38(12), 3610–3620. https://doi.org/10.1080/07391102.2019.1664937
   PubMed Web of Science ®Google Scholar
• Hubbard, R. E., & Haider, M. K. (2010). Hydrogen bonds in proteins: role and strength. eLS
   Google Scholar
• Khan, A., Mohammad, T., Shamsi, A., Hussain, A., Alajmi, M. F., Husain, S. A., Iqbal, M. A., & Hassan, M. I. (2021). Identification of plant-based hexokinase 2 inhibitors: Combined molecular docking and dynamics simulation studies. Journal of Biomolecular Structure and Dynamics, 1–13. https://doi.org/10.1080/07391102.2021.1942217
   Google Scholar
• Kim, H.-H., Hyun, J.-S., Choi, J., Choi, K.-E., Jee, J.-G., & Park, S. J. (2018). Structural ensemble-based docking simulation and biophysical studies discovered new inhibitors of Hsp90 N-terminal domain. Scientific Reports, 8(1), 1–13. https://doi.org/10.1038/s41598-017-18332-8
   PubMed Web of Science ®Google Scholar
• Kontoyianni, M. (2017). Docking and virtual screening in drug discovery. Proteomics for drug discovery., Springer. 255–266.
   Google Scholar
• Koparde, A. A., Doijad, R. C., & Magdum, C. S. (2019). Natural products in drug discovery. In Pharmacognosy-medicinal plants. IntechOpen.
   Google Scholar
• Lagunin, A., Stepanchikova, A., Filimonov, D., & Poroikov, V. (2000). PASS: Prediction of activity spectra for biologically active substances. Bioinformatics (Oxford, England), 16(8), 747–748. https://doi.org/10.1093/bioinformatics/16.8.747
   PubMed Web of Science ®Google Scholar
• Lobanov, M. Y., Bogatyreva, N., & Galzitskaya, O. (2008). Radius of gyration as an indicator of protein structure compactness. Molecular Biology, 42(4), 623–628. https://doi.org/10.1134/S0026893308040195
   Web of Science ®Google Scholar
• Łukasik, P., Załuski, M., & Gutowska, I. (2021). Cyclin-dependent kinases (CDK) and their role in diseases development–review. International Journal of Molecular Sciences, 22(6), 2935. https://doi.org/10.3390/ijms22062935
   PubMed Web of Science ®Google Scholar
• Ma, H., Seebacher, N. A., Hornicek, F. J., & Duan, Z. (2019). Cyclin-dependent kinase 9 (CDK9) is a novel prognostic marker and therapeutic target in osteosarcoma. EBioMedicine, 39, 182–193. https://doi.org/10.1016/j.ebiom.2018.12.022
   PubMed Web of Science ®Google Scholar
• Maisuradze, G. G., Liwo, A., & Scheraga, H. A. (2009). Principal component analysis for protein folding dynamics. Journal of Molecular Biology, 385(1), 312–329. https://doi.org/10.1016/j.jmb.2008.10.018
   PubMed Web of Science ®Google Scholar
• Mallamace, F., Corsaro, C., Mallamace, D., Vasi, S., Vasi, C., Baglioni, P., Buldyrev, S. V., Chen, S.-H., & Stanley, H. E. (2016). Energy landscape in protein folding and unfolding. Proceedings of the National Academy of Sciences of the United States of America, 113(12), 3159–3163. https://doi.org/10.1073/pnas.1524864113
   PubMed Web of Science ®Google Scholar
• Malumbres, M. (2014). Cyclin-dependent kinases. Genome Biology, 15(6), 122–110. https://doi.org/10.1186/gb4184
   PubMed Web of Science ®Google Scholar
• Mark, P., & Nilsson, L. (2001). Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K. The Journal of Physical Chemistry A, 105(43), 9954–9960. https://doi.org/10.1021/jp003020w
   Web of Science ®Google Scholar
• Mazola, Y., Guirola, O., Palomares, S., Chinea, G., Menéndez, C., Hernández, L., & Musacchio, A. (2015). A comparative molecular dynamics study of thermophilic and mesophilic β-fructosidase enzymes. Journal of Molecular Modeling, 21(9), 228. https://doi.org/10.1007/s00894-015-2772-4
   PubMed Web of Science ®Google Scholar
• Mitscher, L. A., Park, Y. H., Clark, D., & Beal, J. L. (1980). Antimicrobial agents from higher plants. Antimicrobial isoflavanoids and related substances from Glycyrrhiza glabra L. var. typica. Journal of Natural Products, 43(2), 259–269. https://doi.org/10.1021/np50008a004
   PubMed Web of Science ®Google Scholar
• Mohammad, T., Mathur, Y., & Hassan, M. I. (2021). InstaDock: A single-click graphical user interface for molecular docking-based virtual high-throughput screening. Briefings in Bioinformatics, 22(4), bbaa279. https://doi.org/10.1093/bib/bbaa279
   PubMed Web of Science ®Google Scholar
• Mohanraj, K., Karthikeyan, B. S., Vivek-Ananth, R., Chand, R. B., Aparna, S., Mangalapandi, P., & Samal, A. (2018). IMPPAT: A curated database of I ndian M edicinal P lants, P hytochemistry A nd T herapeutics. Scientific Reports, 8(1), 1–17. https://doi.org/10.1038/s41598-018-22631-z
   PubMed Web of Science ®Google Scholar
• Napolitano, G., Majello, B., Licciardo, P., Giordano, A., & Lania, L. (2000). Transcriptional activity of positive transcription elongation factor b kinase in vivo requires the C-terminal domain of RNA polymerase II. Gene, 254(1–2), 139–145. https://doi.org/10.1016/s0378-1119(00)00278-x
   PubMedGoogle Scholar
• Naqvi, A. A., Mohammad, T., Hasan, G. M., & Hassan, M. (2018). Advancements in docking and molecular dynamics simulations towards ligand-receptor interactions and structure-function relationships. Current Topics in Medicinal Chemistry, 18(20), 1755–1768. https://doi.org/10.2174/1568026618666181025114157
   PubMed Web of Science ®Google Scholar
• Pires, D. E., Blundell, T. L., & Ascher, D. B. (2015). pkCSM: predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. Journal of Medicinal Chemistry, 58(9), 4066–4072. https://doi.org/10.1021/acs.jmedchem.5b00104
   PubMed Web of Science ®Google Scholar
• Reddy, L., Odhav, B., & Bhoola, K. (2003). Natural products for cancer prevention: A global perspective. Pharmacology & Therapeutics, 99(1), 1–13. https://doi.org/10.1016/s0163-7258(03)00042-1
   PubMed Web of Science ®Google Scholar
• Richmond, T. J. (1984). Solvent accessible surface area and excluded volume in proteins: Analytical equations for overlapping spheres and implications for the hydrophobic effect. Journal of Molecular Biology, 178(1), 63–89. https://doi.org/10.1016/0022-2836(84)90231-6
   PubMed Web of Science ®Google Scholar
• Schüttelkopf, A. W., & Van Aalten, D. M. (2004). PRODRG: a tool for high-throughput crystallography of protein–ligand complexes. Acta Crystallographica. Section D, Biological Crystallography, 60(Pt 8), 1355–1363. https://doi.org/10.1107/S0907444904011679
   PubMedGoogle Scholar
• Seeliger, D., & De Groot, B. L. (2010). Conformational transitions upon ligand binding: Holo-structure prediction from apo conformations. PLoS Computational Biology, 6(1), e1000634. https://doi.org/10.1371/journal.pcbi.1000634
   PubMed Web of Science ®Google Scholar
• Tahirov, T. H., Babayeva, N. D., Varzavand, K., Cooper, J. J., Sedore, S. C., & Price, D. H. (2010). Crystal structure of HIV-1 Tat complexed with human P-TEFb. Nature, 465(7299), 747–751. https://doi.org/10.1038/nature09131
   PubMed Web of Science ®Google Scholar
• Turkson, J. (2017). Cancer drug discovery and anticancer drug development. In The molecular basis of human cancer (pp. 695–707). Springer.
   Google Scholar
• Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718. https://doi.org/10.1002/jcc.20291
   PubMed Web of Science ®Google Scholar
• Wang, Y., Dow, E. C., Liang, Y.-Y., Ramakrishnan, R., Liu, H., Sung, T.-L., Lin, X., & Rice, A. P. (2008). Phosphatase PPM1A regulates phosphorylation of Thr-186 in the Cdk9 T-loop. The Journal of Biological Chemistry, 283(48), 33578–33584. https://doi.org/10.1074/jbc.M807495200
   PubMed Web of Science ®Google Scholar
• Williams, M., & Ladbury, J. (2003). Hydrogen bonds in protein-ligand complexes. Methods and Principles in Medicinal Chemistry, 19, 137–137.
   Google Scholar
• Yamada, T., & Sugimoto, K. (2016). Guggulsterone and its role in chronic diseases. In Drug discovery from mother nature (pp. 329–361). Cham: Springer.
   Google Scholar