73
Views
0
CrossRef citations to date
0
Altmetric
Research Article

Natural compounds inhibit Monkeypox virus methyltransferase VP39 in silico studies

, ORCID Icon, , , , & show all
Received 30 Sep 2023, Accepted 15 Feb 2024, Published online: 28 Feb 2024

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
  • Alakunle, E. F., & Okeke, M. I. (2022). Monkeypox virus: A neglected zoonotic pathogen spreads globally. Nature Reviews Microbiology, 20(9), 507–508. https://doi.org/10.1038/s41579-022-00776-z
  • Aliev, A. E., Kulke, M., Khaneja, H. S., Chudasama, V., Sheppard, T. D., & Lanigan, R. M. (2014). Motional timescale predictions by molecular dynamics simulations: Case study using proline and hydroxyproline sidechain dynamics. Proteins: Structure, Function, and Bioinformatics, 82(2), 195–215. https://doi.org/10.1002/prot.24350
  • Almlöf, M., Brandsdal, B. O., & Aqvist, J. (2004). Binding affinity prediction with different force fields: Examination of the linear interaction energy method. Journal of Computational Chemistry, 25(10), 1242–1254. https://doi.org/10.1002/jcc.20047
  • Baell, J. B. J. A. M C L. (2015). Screening-based translation of public research encounters painful problems. ACS Medicinal Chemistry Letters, 6(3), 229–234.https://doi.org/10.1021/acsmedchemlett.5b00032
  • Baell, J. B., & Holloway, G. A. J. J. O M C (2010). New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays. Journal of Medicinal Chemistry, 53(7), 2719–2740. https://doi.org/10.1021/jm901137j
  • 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
  • Bisson, J., McAlpine, J. B., Friesen, J. B., Chen, S.-N., Graham, J., & Pauli, G. F. J. J. O M C (2016). Can invalid bioactives undermine natural product-based drug discovery? Journal of Medicinal Chemistry, 59(5), 1671–1690. https://doi.org/10.1021/acs.jmedchem.5b01009
  • Bjelic, S., Nervall, M., Gutiérrez-de-Terán, H., Ersmark, K., Hallberg, A., & Aqvist, J. (2007). Computational inhibitor design against malaria plasmepsins. Cellular and Molecular Life Sciences: CMLS, 64(17), 2285–2305. https://doi.org/10.1007/s00018-007-7102-2
  • Bunge, E. M., Hoet, B., Chen, L., Lienert, F., Weidenthaler, H., Baer, L. R., & Steffen, R. (2022). The changing epidemiology of human monkeypox—A potential threat? A systematic review. PLoS Neglected Tropical Diseases, 16(2), e0010141. https://doi.org/10.1371/journal.pntd.0010141
  • Case, D. A., Ben-Shalom, I. Y., Brozell, S. R., Cerutti, D. S., Cheatham, T. E., Cruzeiro, I. V. W. D., Darden, T. A., Duke, R. E., Ghoreishi D., Gilson, M. K., Gohlke, H., Goetz, A. W., Greene, D., Harris, R., Homeyer, N., Huang, Y., Izadi, S., Kovalenko, A., Kurtzman X., … Xiao, L., York, D. M., Kollman, P. A. (2018). AMBER 18. University of California.
  • ChemAxon. (2023). Chemicalize was used for prediction of chemical properties. https://chemicalize.com/
  • Cho, C. T., & Wenner, H. A. (1973). Monkeypox virus. Bacteriological Reviews, 37(1), 1–18. https://doi.org/10.1128/br.37.1.1-18.1973
  • Decherchi, S., & Cavalli, A. (2020). Thermodynamics and kinetics of drug-target binding by molecular simulation. Chemical Reviews, 120(23), 12788–12833. https://doi.org/10.1021/acs.chemrev.0c00534
  • DeLaurentis, C. E., Kiser, J., & Zucker, J. (2022). New perspectives on antimicrobial agents: Tecovirimat for treatment of human monkeypox virus. Antimicrobial Agents and Chemotherapy, 66(12), e01226-22. https://doi.org/10.1128/aac.01226-22
  • Dou, Y. M., Yuan, H., & Tian, H. W. (2023). Monkeypox virus: Past and present. World Journal of Pediatrics, 19(3), 224–230. https://doi.org/10.1007/s12519-022-00618-1
  • Efron, B. (1979). Bootstrap methods: Another kook at the Jackknife. Annals of Statistics, 7, 1–26. https://doi.org/10.1214/aos/1176344552
  • Elsayed, S., Bondy, L., & Hanage, W. P. (2022). Monkeypox virus infections in humans. Clinical Microbiology Reviews, 35(4), e00092-22. https://doi.org/10.1128/cmr.00092-22
  • Farlow, J., Ichou, M. A., Huggins, J., & Ibrahim, S. (2010). Comparative whole genome sequence analysis of wild-type and cidofovir-resistant monkeypoxvirus. Virology Journal, 7(1), 110. https://doi.org/10.1186/1743-422X-7-110
  • Fox, T., & Kollman, P. A. (1998). Application of the RESP methodology in the parametrization of organic solvents. The Journal of Physical Chemistry B, 102(41), 8070–8079. https://doi.org/10.1021/jp9717655
  • Gong, Q., Wang, C., Chuai, X., & Chiu, S. (2022). Monkeypox virus: A re-emergent threat to humans. Virologica Sinica, 37(4), 477–482. https://doi.org/10.1016/j.virs.2022.07.006
  • Gutiérrez-de-Terán, H., & Åqvist, J. (2012). Linear interaction energy: Method and applications in drug design. In R. Baron (Ed.), Computational drug discovery and design (Vol. 819, pp. 305–323). MDPI AG.
  • Hansson, T., Marelius, J., & Aqvist, J. (1998). Ligand binding affinity prediction by linear interaction energy methods. Journal of Computer-Aided Molecular Design, 12(1), 27–35. https://doi.org/10.1023/a:1007930623000
  • Head-Gordon, M., Pople, J. A., & Frisch, M. J. (1988). MP2 energy evaluation by direct methods. Chemical Physics Letters, 153(6), 503–506. https://doi.org/10.1016/0009-2614(88)85250-3
  • Hodel, A. E., Gershon, P. D., Shi, X., & Quiocho, F. A. (1996). The 1.85 Å structure of vaccinia protein VP39: A bifunctional enzyme that participates in the modification of both mRNA ends. Cell, 85(2), 247–256. https://doi.org/10.1016/S0092-8674(00)81101-0
  • Homeyer, N., Stoll, F., Hillisch, A., & Gohlke, H. (2014). Binding free energy calculations for lead optimization: Assessment of their accuracy in an industrial drug design context. Journal of Chemical Theory and Computation, 10(8), 3331–3344. https://doi.org/10.1021/ct5000296
  • Huang, Y., Mu, L., & Wang, W. (2022). Monkeypox: Epidemiology, pathogenesis, treatment and prevention. Signal Transduction and Targeted Therapy, 7(1), 373. https://doi.org/10.1038/s41392-022-01215-4
  • Lansiaux, E., Jain, N., Laivacuma, S., & Reinis, A. (2022). The virology of human monkeypox virus (hMPXV): A brief overview. Virus Research, 322, 198932. https://doi.org/10.1016/j.virusres.2022.198932
  • Lee, S. K., Lee, I. H., Kim, H. J., Chang, G. S., Chung, J. E., & No, K. T. (2003). The PreADME approach: Web-based program for rapid prediction of physico-chemical, drug absorption and drug-like properties, EuroQSAR 2002 designing drugs and crop protectants: Processes, problems and solutions (pp. 418–420). Malden, MA.
  • Li, H., Zhang, H., Ding, K., Wang, X.-H., Sun, G.-Y., Liu, Z.-X., & Luo, Y. (2022). The evolving epidemiology of monkeypox virus. Cytokine & Growth Factor Reviews, 68, 1–12. https://doi.org/10.1016/j.cytogfr.2022.10.002
  • Lum, F.-M., Torres-Ruesta, A., Tay, M. Z., Lin, R. T., Lye, D. C., Rénia, L., & Ng, L. F. (2022). Monkeypox: Disease epidemiology, host immunity and clinical interventions. Nature Reviews. Immunology, 22(10), 597–613. https://doi.org/10.1038/s41577-022-00775-4
  • Marshall, G. R. (1987). Computer-aided drug design. Annual Review of Pharmacology and Toxicology, 27(1), 193–213. https://doi.org/10.1146/annurev.pa.27.040187.001205
  • Møller, C., & Plesset, M. S. (1934). Note on an approximation treatment for many-electron systems. Physical Review, 46(7), 618–622. https://doi.org/10.1103/PhysRev.46.618
  • NCI, (2021). NCI Diversity Set VII Information. https://dtp.cancer.gov/organization/dscb/obtaining/available_plates.htm (accessed May 24).
  • 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. https://doi.org/10.1021/acs.jnatprod.5b01055
  • Ngo, S. T., Mai, B. K., Derreumaux, P., & Vu, V. V. (2019). Adequate prediction for inhibitor affinity of Aβ40 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. (2020). Oversampling free energy perturbation simulation in determination of the ligand-binding free energy. Journal of Computational Chemistry, 41(7), 611–618. https://doi.org/10.1002/jcc.26130
  • Ngo, S. T., Nguyen, T. H., Tung, N. T., Vu, V. V., Pham, M. Q., & Mai, B. K. (2022). Characterizing the ligand-binding affinity toward SARS-CoV-2 Mpro via physics- and knowledge-based approaches. Physical Chemistry Chemical Physics, 24(48), 29266–29278. https://doi.org/10.1039/d2cp04476e
  • Ngo, S. T., Quynh Anh Pham, N., Thi Le, L., Pham, D. H., & Vu, V. V. (2020). Computational determination of potential inhibitors of SARS-CoV-2 main protease. Journal of Chemical Information and Modeling, 60(12), 5771–5780. https://doi.org/10.1021/acs.jcim.0c00491
  • Ngo, S. T., Tam, N. M., Pham, M. Q., & Nguyen, T. H. (2021). Benchmark of popular free energy approaches revealing the inhibitors binding to SARS-CoV-2 mpro. Journal of Chemical Information and Modeling, 61(5), 2302–2312. https://doi.org/10.1021/acs.jcim.1c00159
  • 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
  • Nguyen, T. H., Tam, N. M., Tuan, M. V., Zhan, P., Vu, V. V., Quang, D. T., & Ngo, S. T. (2023). Searching for potential inhibitors of SARS-COV-2 main protease using supervised learning and perturbation calculations. Chemical Physics, 564, 111709. https://doi.org/10.1016/j.chemphys.2022.111709
  • Pham, H. T. N., & Phung, H. T. T. (2023). Comparing the performance of molecular docking tools for HIV-1 protease inhibitors. Journal of Advanced Engineering and Computation, 7(2), 95. https://doi.org/10.55579/jaec.202372.400
  • Pham, T. N. H., Nguyen, T. H., Tam, N. M., Y. Vu, T., Pham, N. T., Huy, N. T., Mai, B. K., Tung, N. T., Pham, M. Q., V. Vu, V., & Ngo, S. T. (2021). Improving ligand-ranking of AutoDock vina by changing the empirical parameters. Journal of Computational Chemistry, 43(3), 160–169. https://doi.org/10.1002/jcc.26779
  • Rizk, J. G., Lippi, G., Henry, B. M., Forthal, D. N., & Rizk, Y. (2022). Prevention and treatment of monkeypox. Drugs, 82(9), 957–963. https://doi.org/10.1007/s40265-022-01742-y
  • Schrödinger, L. L. C. (2020). P. Schrödinger release 2020-4: Maestro. Schrödinger, L. L. C.
  • Silhan, J., Klima, M., Chalupska, D., Kozic, J., & Boura, E. (2022). The structure of monkeypox virus 2′-O-ribose methyltransferase VP39 in complex with sinefungin provides the foundation for inhibitor design. bioRxiv, 2022.09. 27.509668. https://doi.org/10.1101/2022.09.27.509668
  • Silhan, J., Klima, M., Otava, T., Skvara, P., Chalupska, D., Chalupsky, K., Kozic, J., Nencka, R., & Boura, E. (2023). Discovery and structural characterization of monkeypox virus methyltransferase VP39 inhibitors reveal similarities to SARS-CoV-2 nsp14 methyltransferase. Nature Communications, 14(1), 2259. https://doi.org/10.1038/s41467-023-38019-1
  • Sousa da Silva, A. W., & Vranken, W. F. (2012). ACPYPE - AnteChamber PYthon Parser interfacE. BMC Research Notes, 5(1), 367. https://doi.org/10.1186/1756-0500-5-367
  • Tam, N. M., Nguyen, T. H., Pham, M. Q., Hong, N. D., Tung, N. T., Vu, V. V., Quang, D. T., & Ngo, S. T. (2023). Upgrading nirmatrelvir to inhibit SARS-CoV-2 Mpro via DeepFrag and free energy calculations. Journal of Molecular Graphics & Modelling, 124, 108535. https://doi.org/10.1016/j.jmgm.2023.108535
  • Tanchuk, V. Y., Tanin, V. O., Vovk, A. I., & Poda, G. (2016). A new, improved hybrid scoring function for molecular docking and scoring based on AutoDock and AutoDock vina. Chemical Biology & Drug Design, 87(4), 618–625. https://doi.org/10.1111/cbdd.12697
  • Thai, Q. M., Pham, T. N. H., Hiep, D. M., Pham, M. Q., Tran, P.-T., Nguyen, T. H., & Ngo, S. T. (2022). Searching for AChE inhibitors from natural compounds by using machine learning and atomistic simulations. Journal of Molecular Graphics & Modelling, 115, 108230. https://doi.org/10.1016/j.jmgm.2022.108230
  • Wang, D. P., Zhao, R., Wang, H. F., Wang, M. Y., Hu, W. S., Lin, M. M., Shu, W., Cao, J. M., Cui, W., & Zhou, X. (2023). Crystal structure of mRNA cap (guanine-N7) methyltransferase E12 subunit from monkeypox virus and discovery of its inhibitors. bioRxiv, 2023.03. 12.532263.
  • Wang, J., Shahed-Ai-Mahmud, M., Chen, A., Li, K., Tan, H., & Joyce, R. (2023). An overview of antivirals against monkeypox virus and other orthopoxviruses. Journal of Medicinal Chemistry, 66(7), 4468–4490. https://doi.org/10.1021/acs.jmedchem.3c00069
  • Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2004). Development and testing of a general amber force field. Journal of Computational Chemistry, 25(9), 1157–1174. https://doi.org/10.1002/jcc.20035
  • WHO. (2022). Multi-country outbreak of monkeypox. WHO.
  • Xiang, Y., & White, A. (2022). Monkeypox virus emerges from the shadow of its more infamous cousin: Family biology matters. Emerging Microbes & Infections, 11(1), 1768–1777. https://doi.org/10.1080/22221751.2022.2095309
  • Yu, W., & MacKerell, A. D. (2017). Computer-aided drug design methods. In P. Sass (Ed.), Antibiotics: Methods and protocols (pp. 85–106). Humana Press.

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.