129
Views
0
CrossRef citations to date
0
Altmetric
Research Articles

Pharmacophore-guided drug design using LdNMT as a model drug target for leishmaniasis

, , & ORCID Icon
Pages 863-875 | Received 12 Jan 2023, Accepted 22 Mar 2023, Published online: 25 Apr 2023

References

  • Banesh, S., Ramakrishnan, V., & Trivedi, V. (2018). Mapping of phosphatidylserine recognition region on CD36 ectodomain. Archives of Biochemistry and Biophysics, 660, 1–10. https://doi.org/10.1016/j.abb.2018.10.005
  • Bhatnagar, R. S., Fütterer, K., Farazi, T. A., Korolev, S., Murray, C. L., Jackson-Machelski, E., Gokel, G. W., Gordon, J. I., & Waksman, G. (1998). Structure of N-myristoyltransferase with bound myristoylCoA and peptide substrate analogs. Nature Structural Biology, 5(12), 1091–1097. https://doi.org/10.1038/4202
  • Brannigan, J. A., Smith, B. A., Yu, Z., Brzozowski, A. M., Hodgkinson, M. R., Maroof, A., Price, H. P., Meier, F., Leatherbarrow, R. J., Tate, E. W., Smith, D. F., & Wilkinson, A. J. (2010). N-myristoyltransferase from Leishmania donovani: Structural and functional characterisation of a potential drug target for visceral leishmaniasis. Journal of Molecular Biology, 396(4), 985–999. https://doi.org/10.1016/j.jmb.2009.12.032
  • Case, D. A., Cheatham, T. E., III, Darden, T., Gohlke, H., Luo, R., Merz, K. M., Jr, Onufriev, A., Simmerling, C., Wang, B., & Woods, R. J. (2005). The Amber biomolecular simulation programs. Journal of Computational Chemistry, 26(16), 1668–1688. https://doi.org/10.1002/jcc.20290
  • Croft, S. L., Sundar, S., & Fairlamb, A. H. (2006). Drug resistance in leishmaniasis. Clinical Microbiology Reviews, 19(1), 111–126. https://doi.org/10.1128/CMR.19.1.111-126.2006
  • Croft, S., & Olliaro, P. (2011). Leishmaniasis chemotherapy—Challenges and opportunities. Clinical Microbiology and Infection: The Official Publication of the European Society of Clinical Microbiology and Infectious Diseases, 17(10), 1478–1483. https://doi.org/10.1111/j.1469-0691.2011.03630.x
  • DeLano, W. L. (2002). Pymol: An open-source molecular graphics tool. CCP4 Newsl. Protein Crystallogr, 40, 82–92.
  • Eswar, N., Eramian, D., Webb, B., Shen, M.-Y., & Sali, A. (2008). Protein structure modeling with MODELLER, structural proteomics (pp. 145–159). Springer.
  • Gupta, G., Oghumu, S., & Satoskar, A. R. (2013). Mechanisms of immune evasion in leishmaniasis. Advances in Applied Microbiology (Vol. 82, pp. 155–184). Elsevier.
  • Hutton, J. A., Goncalves, V., Brannigan, J. A., Paape, D., Wright, M. H., Waugh, T. M., Roberts, S. M., Bell, A. S., Wilkinson, A. J., Smith, D. F., Leatherbarrow, R. J., & Tate, E. W. (2014). Structure-based design of potent and selective Leishmania N-myristoyltransferase inhibitors. Journal of Medicinal Chemistry, 57(20), 8664–8670. https://doi.org/10.1021/jm5011397
  • Jin, Y., Smith, C. L., Hu, L., Campanale, K. M., Stoltz, R., Huffman, L. G., McNearney, T. A., Yang, X. Y., Ackermann, B. L., Dean, R., Regev, A., & Landschulz, W. (2016). Pharmacodynamic comparison of LY3023703, a novel microsomal prostaglandin e synthase 1 inhibitor, with celecoxib. Clinical Pharmacology and Therapeutics, 99(3), 274–284. https://doi.org/10.1002/cpt.260
  • Jo, S., Kim, T., Iyer, V. G., & Im, W. (2008). CHARMM‐GUI: A web‐based graphical user interface for CHARMM. Journal of Computational Chemistry, 29(11), 1859–1865. https://doi.org/10.1002/jcc.20945
  • Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., Bridgland, A., Meyer, C., Kohl, S. A. A., Ballard, A. J., Cowie, A., Romera-Paredes, B., Nikolov, S., Jain, R., Adler, J., … Hassabis, D. (2021). Highly accurate protein structure prediction with AlphaFold. Nature, 596(7873), 583–589. https://doi.org/10.1038/s41586-021-03819-2
  • Khan, D. A., Hamdani, S. D. A., Iftikhar, S., Malik, S. Z., Zaidi, N-u-SS., Gul, A., Babar, M. M., Ozturk, M., Turkyilmaz Unal, B., & Gonenc, T. (2022). Pharmacoinformatics approaches in the discovery of drug-like antimicrobials of plant origin. Journal of Biomolecular Structure and Dynamics, 40(16), 7612–7628. https://doi.org/10.1080/07391102.2021.1894982
  • Kumar, S., & Ayyannan, S. R. (2022). Identification of new small molecule monoamine oxidase-B inhibitors through pharmacophore-based virtual screening, molecular docking and molecular dynamics simulation studies. Journal of Biomolecular Structure and Dynamics, 1–22. https://doi.org/10.1080/07391102.2022.2112082
  • Laskowski, R., MacArthur, M., & Thornton, J. (2006). PROCHECK: Validation of protein-structure coordinates.
  • Lauro, G., Terracciano, S., Cantone, V., Ruggiero, D., Fischer, K., Pace, S., Werz, O., Bruno, I., & Bifulco, G. (2020). A combinatorial virtual screening approach driving the synthesis of 2, 4‐thiazolidinedione‐based molecules as new dual mPGES‐1/5‐LO inhibitors. ChemMedChem, 15(6), 481–489. https://doi.org/10.1002/cmdc.201900694
  • Lee, H. S., & Im, W. (2016). G‐LoSA: An efficient computational tool for local structure‐centric biological studies and drug design. Protein Science: A Publication of the Protein Society, 25(4), 865–876. https://doi.org/10.1002/pro.2890
  • Liu, T., & Altman, R. B. (2011). Using multiple microenvironments to find similar ligand-binding sites: Application to kinase inhibitor binding. PLoS Computational Biology, 7(12), e1002326. https://doi.org/10.1371/journal.pcbi.1002326
  • Lu, G., & Moriyama, E. N. (2004). Vector NTI, a balanced all-in-one sequence analysis suite. Briefings in Bioinformatics, 5(4), 378–388. https://doi.org/10.1093/bib/5.4.378
  • 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. https://doi.org/10.1002/jcc.21256
  • Moser, D., Wisniewska, J. M., Hahn, S., Achenbach, J., Buscató, E. L., Klingler, F.-M., Hofmann, B., Steinhilber, D., & Proschak, E. (2012). Dual-target virtual screening by pharmacophore elucidation and molecular shape filtering. ACS Medicinal Chemistry Letters, 3(2), 155–158. https://doi.org/10.1021/ml200286e
  • Paape, D., Prendergast, C. T., Price, H. P., Doehl, J. S., & Smith, D. F. (2020). Genetic validation of Leishmania genes essential for amastigote survival in vivo using N-myristoyltransferase as a model. Parasites & Vectors, 13(1), 1–16. https://doi.org/10.1186/s13071-020-3999-1
  • Pihan, E., Colliandre, L., Guichou, J.-F., & Douguet, D. (2012). e-Drug3D: 3D structure collections dedicated to drug repurposing and fragment-based drug design. Bioinformatics (Oxford, England), 28(11), 1540–1541. https://doi.org/10.1093/bioinformatics/bts186
  • Price, H. P., Menon, M. R., Panethymitaki, C., Goulding, D., McKean, P. G., & Smith, D. F. (2003). Myristoyl-CoA: Protein N-myristoyltransferase, an essential enzyme and potential drug target in kinetoplastid parasites. The Journal of Biological Chemistry, 278(9), 7206–7214. https://doi.org/10.1074/jbc.M211391200
  • Salentin, S., Schreiber, S., Haupt, V. J., Adasme, M. F., & Schroeder, M. (2015). PLIP: Fully automated protein–ligand interaction profiler. Nucleic Acids Research, 43(W1), W443–W447. https://doi.org/10.1093/nar/gkv315
  • Souza, B., Lacerda, P. S., Pita, S., Kato, R. B., & Leite, F. H. A. (2021). Identification of potential Leishmania chagasi superoxide dismutase allosteric modulators by structure-based computational approaches: Homology modelling, molecular dynamics and pharmacophore-based virtual screening. Journal of Biomolecular Structure & Dynamics, 39(18), 7000–7016. https://doi.org/10.1080/07391102.2020.1804453
  • Stäger, S., Joshi, T., & Bankoti, R. (2010). Immune evasive mechanisms contributing to persistent Leishmania donovani infection. Immunologic Research, 47(1–3), 14–24. https://doi.org/10.1007/s12026-009-8135-4
  • Sun, T., Chen, Y., Wen, Y., Zhu, Z., & Li, M. (2021). Prempli: A machine learning model for predicting the effects of missense mutations on protein-ligand interactions. Communications Biology, 4(1), 11. https://doi.org/10.1038/s42003-021-02826-3
  • Tate, E. W., Bell, A. S., Rackham, M. D., & Wright, M. H. (2014). N-myristoyltransferase as a potential drug target in malaria and leishmaniasis. Parasitology, 141(1), 37–49. https://doi.org/10.1017/S0031182013000450
  • Wallace, A. C., Laskowski, R. A., & Thornton, J. M. (1995). LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Engineering, 8(2), 127–134. https://doi.org/10.1093/protein/8.2.127
  • Wang, Z., Pan, H., Sun, H., Kang, Y., Liu, H., Cao, D., & Hou, T. (2022). fastDRH: A webserver to predict and analyze protein–ligand complexes based on molecular docking and MM/PB (GB) SA computation. Briefings in Bioinformatics, 23(5). https://doi.org/10.1093/bib/bbac201
  • Wright, M. H., Paape, D., Storck, E. M., Serwa, R. A., Smith, D. F., & Tate, E. W. (2015). Global analysis of protein N-myristoylation and exploration of N-myristoyltransferase as a drug target in the neglected human pathogen Leishmania donovani. Chemistry & Biology, 22(3), 342–354. https://doi.org/10.1016/j.chembiol.2015.01.003
  • Yang, J., Yan, R., Roy, A., Xu, D., Poisson, J., & Zhang, Y. (2015). The I-TASSER suite: Protein structure and function prediction. Nature Methods, 12(1), 7–8. https://doi.org/10.1038/nmeth.3213
  • Yang, S.-Y. (2010). Pharmacophore modeling and applications in drug discovery: Challenges and recent advances. Drug Discovery Today, 15(11–12), 444–450. https://doi.org/10.1016/j.drudis.2010.03.013
  • Yuan, S., Chan, H. S., & Hu, Z. (2017). Using PyMOL as a platform for computational drug design. Wiley Interdisciplinary Reviews: Computational Molecular Science, 7, e1298.

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.