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Research Article

Calculation of binding affinity of JAK1 inhibitors via accurately computational estimation

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Pages 7224-7234 | Received 24 Jan 2022, Accepted 23 Aug 2022, Published online: 07 Sep 2022

References

  • Almlöf, M., Brandsdal, B. O., & Åqvist, J. (2004). Binding affinity prediction with different force fields: examination of the linear interaction energy method. Journal of Computational Chemistry, 25(10), 1242–1254.
  • Aqvist, J., & Marelius, J. (2001). The linear interaction energy method for predicting ligand binding free energies. Combinatorial Chemistry & High Throughput Screening, 4(8), 613–626. https://doi.org/10.2174/1386207013330661
  • Åqvist, J., Luzhkov, V. B., & Brandsdal, B. O. (2002). Ligand binding affinities from MD simulations. Accounts of Chemical Research, 35(6), 358–365.
  • Åqvist, J., Medina, C., & Samuelsson, J.-E. (1994). A new method for predicting binding affinity in computer-aided drug design. Protein Engineering, Design and Selection, 7(3), 385–391. https://doi.org/10.1093/protein/7.3.385
  • Bayly, C. I., Cieplak, P., Cornell, W., & Kollman, P. A. (1993). A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. The Journal of Physical Chemistry, 97(40), 10269–10280. https://doi.org/10.1021/j100142a004
  • Buchert, M., Burns, C., & Ernst, M. (2016). Targeting JAK kinase in solid tumors: Emerging opportunities and challenges. Oncogene, 35(8), 939–951.
  • Cao, D. T., Huong Doan, T. M., Pham, V. C., Minh Le, T. H., Chae, J.-W., Yun, H.-Y., Na, M.-K., Kim, Y.-H., Pham, M. Q., & Nguyen, V. H. (2021). Molecular design of anticancer drugs from marine fungi derivatives. RSC Advances, 11(33), 20173–20179.
  • Capoferri, L., van Dijk, M., Rustenburg, A. S., Wassenaar, T. A., Kooi, D. P., & Rifai, E. A. (2017). eTOX ALLIES: an automated pipeLine for linear interaction energy-based simulations. Journal of Cheminformatics, 9, 1–13.
  • Case, D. A., Ben-Shalom, I. Y., Brozell, S. R., Cerutti, D. S., Cheatham, T. E., Cruzeiro, V. W. D. (2018). AMBER (Vol. 18). University of California.
  • Debbab, A., Aly, A. H., Lin, W. H., & Proksch, P. (2010). Bioactive compounds from marine bacteria and fungi. Microbial Biotechnology, 3(5), 544–563.
  • Deshmukh, S. K., Prakash, V., & Ranjan, N. (2017). Marine fungi: A source of potential anticancer compounds. Frontiers in Microbiology, 8, 2536. https://doi.org/10.3389/fmicb.2017.02536
  • Faulkner, D. J., & Marine, p (2000). Marine pharmacology. Antonie Van Leeuwenhoek. 77(2), 135–145. https://doi.org/10.1023/a:1002405815493
  • Forli, S., Huey, R., Pique, M. E., Sanner, M. F., Goodsell, D. S., & Olson, A. J. (2016). Computational protein–ligand docking and virtual drug screening with the AutoDock suite. Nature Protocols, 11(5), 905–919.
  • Gadina, M., Hilton, D., Johnston, J. A., Morinobu, A., Lighvani, A., Zhou, Y. J., Visconti, R., & O’Shea, J. J. (2001). Signaling by type I and II cytokine receptors: Ten years after. Current Opinion in Immunology, 13(3), 363–373.
  • Gasteiger, J., & Marsili, M. (1978). A new model for calculating atomic charges in molecules. Tetrahedron Letters, 19(34), 3181–3184. https://doi.org/10.1016/S0040-4039(01)94977-9
  • Gasteiger, J., & Marsili, M. (1980). Iterative partial equalization of orbital electronegativity—a rapid access to atomic charges. Tetrahedron, 36(22), 3219–3228. https://doi.org/10.1016/0040-4020(80)80168-2
  • Genheden, S., & Ryde, U. (2011). Comparison of the efficiency of the LIE and MM/GBSA methods to calculate ligand-binding energies. Journal of Chemical Theory and Computation, 7(11), 3768–3778.
  • Genheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery, 10(5), 449–461. https://doi.org/10.1517/17460441.2015.1032936
  • Haefner, B. (2003). Drugs from the deep: marine natural products as drug candidates. Drug Discovery Today. 8(12), 536–544.
  • Hurley, C. A., Blair, W. S., Bull, R. J., Chang, C., Crackett, P. H., Deshmukh, G., Dyke, H. J., Fong, R., Ghilardi, N., Gibbons, P., Hewitt, P. R., Johnson, A., Johnson, T., Kenny, J. R., Kohli, P. B., Kulagowski, J. J., Liimatta, M., Lupardus, P. J., Maxey, R. J., … Zak, M. (2013). Novel triazolo-pyrrolopyridines as inhibitors of Janus kinase 1. Bioorganic & Medicinal Chemistry Letters, 23(12), 3592–3598.
  • Jones-Hertzog, D. K., & Jorgensen, W. L. (1997). Binding affinities for sulfonamide inhibitors with human thrombin using Monte Carlo simulations with a linear response method. Journal of Medicinal Chemistry, 40(10), 1539–1549.
  • Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. Journal of Chemical Physics, 79(2), 926–935. https://doi.org/10.1063/1.445869
  • Khalifa, S. A. M., Elias, N., Farag, M. A., Chen, L., Saeed, A., Hegazy, M.-E F., Moustafa, M. S., Abd El-Wahed, A., Al-Mousawi, S. M., Musharraf, S. G., Chang, F.-R., Iwasaki, A., Suenaga, K., Alajlani, M., Göransson, U., & El-Seedi, H. R. (2019). Marine natural products: A source of novel anticancer drugs. Marine Drugs, 17(9), 491. https://doi.org/10.3390/md17090491
  • Kirkwood, J. G. (1935). Statistical mechanics of fluid mixtures. Journal of Chemical Physics, 3(5), 300–313. https://doi.org/10.1063/1.1749657
  • Kuhn, B., & Kollman, P. A. (2000). Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models. Journal of Medicinal Chemistry, 43(20), 3786–3791.
  • Kulagowski, J. J., Blair, W., Bull, R. J., Chang, C., Deshmukh, G., Dyke, H. J., Eigenbrot, C., Ghilardi, N., Gibbons, P., Harrison, T. K., Hewitt, P. R., Liimatta, M., Hurley, C. A., Johnson, A., Johnson, T., Kenny, J. R., Bir Kohli, P., Maxey, R. J., Mendonca, R., … Zak, M. (2012). Identification of imidazo-pyrrolopyridines as novel and potent JAK1 inhibitors. Journal of Medicinal Chemistry, 55(12), 5901–5921.
  • Labadie, S., Barrett, K., Blair, W. S., Chang, C., Deshmukh, G., Eigenbrot, C., Gibbons, P., Johnson, A., Kenny, J. R., Kohli, P. B., Liimatta, M., Lupardus, P. J., Shia, S., Steffek, M., Ubhayakar, S., van Abbema, A., & Zak, M. (2013). Design and evaluation of novel 8-oxo-pyridopyrimidine Jak1/2 inhibitors. Bioorganic & Medicinal Chemistry Letters, 23(21), 5923–5930.
  • Labadie, S., Dragovich, P. S., Barrett, K., Blair, W. S., Bergeron, P., Chang, C., Deshmukh, G., Eigenbrot, C., Ghilardi, N., Gibbons, P., Hurley, C. A., Johnson, A., Kenny, J. R., Kohli, P. B., Kulagowski, J. J., Liimatta, M., Lupardus, P. J., Mendonca, R., Murray, J. M., … Zak, M. (2012). Structure-based discovery of C-2 substituted imidazo-pyrrolopyridine JAK1 inhibitors with improved selectivity over JAK2. Bioorganic & Medicinal Chemistry Letters, 22(24), 7627–7633.
  • Leroy, E., & Constantinescu, S. N. (2017). Rethinking JAK2 inhibition: towards novel strategies of more specific and versatile janus kinase inhibition. Leukemia, 31(5), 1023–1038. https://doi.org/10.1038/leu.2017.43
  • Lindorff-Larsen, K., Piana, S., Palmo, K., Maragakis, P., Klepeis, J. L., Dror, R. O., & Shaw, D. E. (2010). Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins, 78(8), 1950–1958.
  • Liu, N., Shang, F., Xi, L., & Huang, Y. (2013). Tetroazolemycins A and B, two new oxazole-thiazole siderophores from deep-sea Streptomyces olivaceus FXJ8. 012. Marine Drugs, 11(5), 1524–1533. https://doi.org/10.3390/md11051524
  • Mai, B. K., & Li, M. S. (2011). Neuraminidase inhibitor R-125489–a promising drug for treating influenza virus: steered molecular dynamics approach. Biochemical and Biophysical Research Communications, 410(3), 688–691.
  • Mai, B. K., Viet, M. H., & Li, M. S. (2010). Top leads for swine influenza A/H1N1 virus revealed by steered molecular dynamics approach. Journal of Chemical Information and Modeling, 50(12), 2236–2247.
  • Mai, N. T., Lan, N. T., Vu, T. Y., Duong, P. T. M., Tung, N. T., & Phung, H. T. T. (2020). Estimation of the ligand-binding free energy of checkpoint kinase 1 via non-equilibrium MD simulations. Journal of Molecular Graphics & Modelling, 100, 107648. https://doi.org/10.1016/j.jmgm.2020.107648
  • Marshall, G. R. (1987). Computer-aided drug design. Annual Review of Pharmacology and Toxicology, 27, 193–213. https://doi.org/10.1146/annurev.pa.27.040187.001205
  • Mascarenhas, J., T.I., Mughal, & Verstovsek, S. (2012). Biology and clinical management of myeloproliferative neoplasms and development of the JAK inhibitor ruxolitinib. Current Medicinal Chemistry, 19(26), 4399–4413. https://doi.org/10.2174/092986712803251511
  • Menet, C. J., Mammoliti, O., & López-Ramos, M. (2015). Progress toward JAK1-selective inhibitors. Future Medicinal Chemistry, 7(2), 203–235.
  • Menet, C. J., Van Rompaey, L., & Geney, R. (2013). Advances in the discovery of selective JAK inhibitors. In Progress in Medicinal Chemistry (Vol. 52, pp. 153–223). Elsevier.
  • Mesa, R. A., Yasothan, U., & Kirkpatrick, P. (2012). Ruxolitinib. Nature Publishing Group.
  • Molinski, T. F., Dalisay, D. S., Lievens, S. L., & Saludes, J. P. (2009). Drug development from marine natural products. Nature Reviews. Drug Discovery, 8(1), 69–85.
  • Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791.
  • Newman, D. J., & Cragg, G. M. (2016). Natural products as sources of new drugs from 1981 to 2014. Journal of Natural Products, 79(3), 629–661.
  • Ngo, S. T., Hung, H. M., & Nguyen, M. T. (2016). Fast and accurate determination of the relative binding affinities of small compounds to HIV‐1 protease using non‐equilibrium work. Journal of Computational Chemistry, 37(31), 2734–2742.
  • Ngo, S. T., Mai, B. K., Derreumaux, P., & Vu, V. V. (2019). Adequate prediction for inhibitor affinity of Aβ 40 protofibril using the linear interaction energy method. RSC Advances, 9(22), 12455–12461. https://doi.org/10.1039/c9ra01177c
  • Ngo, S. T., Nguyen, T. H., Tung, N. T., Nam, P. C., Vu, K. B., & Vu, V. V. (2020a). Oversampling free energy perturbation simulation in determination of the ligand-binding free energy. Journal of Computational Chemistry, 41(7), 611–618.
  • Ngo, S. T., Quynh Anh Pham, N., Thi Le, L., Pham, D.-H., & Vu, V. V. (2020b). Computational determination of potential inhibitors of SARS-CoV-2 main protease. Journal of Chemical Information and Modeling, 60(12), 5771–5780.
  • Nguyen, N. T., Nguyen, T. H., Pham, T. N. H., Huy, N. T., Bay, M. V., Pham, M. Q., Nam, P. C., Vu, V. V., & Ngo, S. T. (2020). Autodock vina adopts more accurate binding poses but autodock4 forms better binding affinity. Journal of Chemical Information and Modeling, 60(1), 204–211. https://doi.org/10.1021/acs.jcim.9b00778
  • O’Shea, J. J., Holland, S. M., & Staudt, L. M. (2013). JAKs and STATs in immunity, immunodeficiency, and cancer. New England Journal of Medicine, 368, 161–170.
  • Pham, M. Q., Vu, K. B., Han Pham, T. N., Thuy Huong, L. T., Tran, L. H., Tung, N. T., Vu, V. V., Nguyen, T. H., & Ngo, S. T. (2020). Rapid prediction of possible inhibitors for SARS-CoV-2 main protease using docking and FPL simulations. RSC Advances, 10(53), 31991–31996.
  • Pham, T. N. H., Nguyen, T. H., Tam, N. M., Vu, Y. T., Pham, N. T., Huy, N. T., Mai, B. K., Tung, N. T., Pham, M. Q., Vu, V., & Ngo, S. T. (2022). Improving ligand‐ranking of AutoDock Vina by changing the empirical parameters. Journal of Computational Chemistry, 43(3), 160–169.
  • Sousa da Silva, A. W., & Vranken, W. F. (2012). ACPYPE – AnteChamber Python Parser interfacE. BMC Research Notes, 5, 1–8.
  • Sun, W., Wu, W., Liu, X., Zaleta-Pinet, D. A., & Clark, B. R. (2019). Bioactive compounds isolated from marine-derived microbes in China: 2009–2018. Marine Drugs, 17(6), 339. https://doi.org/10.3390/md17060339
  • Tam, N. M., Nam, P. C., Quang, D. T., Tung, N. T., Vu, V. V., & Ngo, S. T. (2021). Binding of inhibitors to the monomeric and dimeric SARS-CoV-2 Mpro. RSC Advances, 11(5), 2926–2934. https://doi.org/10.1039/D0RA09858B
  • Uciechowska, U., Schemies, J., Scharfe, M., Lawson, M., Wichapong, K., Jung, M., & Sippl, W. (2012). Binding free energy calculations and biological testing of novel thiobarbiturates as inhibitors of the human NAD + dependent histone deacetylase Sirt2. MedChemComm, 3(2), 167–173. https://doi.org/10.1039/C1MD00214G
  • Verma, A., Kambhampati, S., Parmar, S., & Platanias, L. C. (2003). Jak family of kinases in cancer. Cancer Metastasis Reviews, 22(4), 423–434.
  • Wu, P., Nielsen, T. E., & Clausen, M. H. (2015). FDA-approved small-molecule kinase inhibitors. Trends in Pharmacological Sciences, 36(7), 422–439.
  • Wu, Z., Liu, D., Huang, J., Proksch, P., Zhu, K., & Lin, W. (2018). Hansforesters A–M, polyesters from the sponge-associated fungus Hansfordia sinuosae with antibacterial activities. RSC Advances, 8(69), 39756–39768. https://doi.org/10.1039/C8RA08606K
  • Yu, W., & MacKerell, A. D., Jr. (2017). Computer-aided drug design methods. Methods in Molecular Biology, 1520, 85–106.
  • Zak, M., Hurley, C. A., Ward, S. I., Bergeron, P., Barrett, K., Balazs, M., Blair, W. S., Bull, R., Chakravarty, P., Chang, C., Crackett, P., Deshmukh, G., DeVoss, J., Dragovich, P. S., Eigenbrot, C., Ellwood, C., Gaines, S., Ghilardi, N., Gibbons, P., … Kulagowski, J. J. (2013). Identification of C-2 hydroxyethyl imidazopyrrolopyridines as potent JAK1 inhibitors with favorable physicochemical properties and high selectivity over JAK2. Journal of Medicinal Chemistry, 56(11), 4764–4785.
  • Zak, M., Mendonca, R., Balazs, M., Barrett, K., Bergeron, P., Blair, W. S., Chang, C., Deshmukh, G., Devoss, J., Dragovich, P. S., Eigenbrot, C., Ghilardi, N., Gibbons, P., Gradl, S., Hamman, C., Hanan, E. J., Harstad, E., Hewitt, P. R., Hurley, C. A., … Xiao, Y. (2012). Discovery and optimization of C-2 methyl imidazopyrrolopyridines as potent and orally bioavailable JAK1 inhibitors with selectivity over JAK2. Journal of Medicinal Chemistry, 55(13), 6176–6193.
  • Zhang, H., Jiang, Y., Cui, Z., & Yin, C. (2018a). Force field benchmark of amino acids. 2. Partition coefficients between water and organic solvents. Journal of Chemical Information and Modeling, 58(8), 1669–1681.
  • Zhang, H., Yin, C., Jiang, Y., & van der Spoel, D. (2018b). Force field benchmark of amino acids: I. Hydration and diffusion in different water models. Journal of Chemical Information and Modeling, 58(5), 1037–1052.
  • Zwanzig, R. W. (1954). High‐temperature equation of state by a perturbation method. I. Nonpolar gases. Journal of Chemical Physics. 22(8), 1420–1426. https://doi.org/10.1063/1.1740409

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