Journal of Computer-Aided Molecular Design

, Volume 23, Issue 6, pp 375–389 | Cite as

Homology modeling and molecular dynamics simulation of N-myristoyltransferase from protozoan parasites: active site characterization and insights into rational inhibitor design

  • Chunquan Sheng
  • Haitao Ji
  • Zhenyuan Miao
  • Xiaoyin Che
  • Jianzhong Yao
  • Wenya Wang
  • Guoqiang Dong
  • Wei Guo
  • Jiaguo Lü
  • Wannian Zhang


Myristoyl-CoA:protein N-myristoyltransferase (NMT) is a cytosolic monomeric enzyme that catalyzes the transfer of the myristoyl group from myristoyl-CoA to the N-terminal glycine of a number of eukaryotic cellular and viral proteins. Recent experimental data suggest NMT from parasites could be a promising new target for the design of novel antiparasitic agents with new mode of action. However, the active site topology and inhibitor specificity of these enzymes remain unclear. In this study, three-dimensional models of NMT from Plasmodium falciparum (PfNMT), Leishmania major (LmNMT) and Trypanosoma brucei (TbNMT) were constructed on the basis of the crystal structures of fungal NMTs using homology modeling method. The models were further refined by energy minimization and molecular dynamics simulations. The active sites of PfNMT, LmNMT and TbNMT were characterized by multiple copy simultaneous search (MCSS). MCSS functional maps reveal that PfNMT, LmNMT and TbNMT share a similar active site topology, which is defined by two hydrophobic pockets, a hydrogen-bonding (HB) pocket, a negatively-charged HB pocket and a positively-charged HB pocket. Flexible docking approaches were then employed to dock known inhibitors into the active site of PfNMT. The binding mode, structure–activity relationships and selectivity of inhibitors were investigated in detail. From the results of molecular modeling, the active site architecture and certain key residues responsible for inhibitor binding were identified, which provided insights for the design of novel inhibitors of parasitic NMTs.


Parasitic N-myristoyltransferase Three-dimensional structures Multiple copy simultaneous search Active sites Flexible molecular docking Ligand selectivity 



This work was supported in part by the National Natural Science Foundation of China (Grant Nos. 30400567) and Shanghai Leading Academic Discipline Project (Project Nos. B906). We thank Dr. Zhanli Wang in NeoTrident Technology LTD. for his assistance in molecular dynamics simulations.


  1. 1.
    Boutin JA (1997) Myristoylation. Cell Signal 9:15. doi: 10.1016/S0898-6568(96)00100-3 CrossRefGoogle Scholar
  2. 2.
    Farazi TA, Waksman G, Gordon JI (2001) The biology and enzymology of protein N-myristoylation. J Biol Chem 276:39501. doi: 10.1074/jbc.R100042200 CrossRefGoogle Scholar
  3. 3.
    Bhatnagar RS, Schall OF, Jackson-Machelski E, Sikorski JA, Devadas B, Gokel GW, Gordon JI (1997) Titration calorimetric analysis of AcylCoA recognition by myristoylCoA:protein N-myristoyltransferase. Biochemistry 36:6700. doi: 10.1021/bi970311v CrossRefGoogle Scholar
  4. 4.
    Rudnick DA, McWherter CA, Rocque WJ, Lennon PJ, Getman DP, Gordon JI (1991) Kinetic and structural evidence for a sequential ordered Bi Bi mechanism of catalysis by Saccharomyces cerevisiae myristoyl-CoA:protein N-myristoyltransferase. J Biol Chem 266:9732Google Scholar
  5. 5.
    Knoll LJ, Johnson DR, Bryant ML, Gordon JI (1995) Functional significance of myristoyl moiety in N-myristoyl proteins. Methods Enzymol 250:405. doi: 10.1016/0076-6879(95)50088-X CrossRefGoogle Scholar
  6. 6.
    Olson EN, Towler DA, Glaser L (1985) Specificity of fatty acid acylation of cellular proteins. J Biol Chem 260:3784Google Scholar
  7. 7.
    Towler DA, Adams SP, Eubanks SR, Towery DS, Jackson-Machelski E, Glaser L, Gordon JI (1987) Purification and characterization of yeast myristoyl CoA:protein N-myristoyltransferase. Proc Natl Acad Sci USA 84:2708. doi: 10.1073/pnas.84.9.2708 CrossRefGoogle Scholar
  8. 8.
    Gordon JI, Duronio RJ, Rudnick DA, Adams SP, Gokel GW (1991) Protein N-myristoylation. J Biol Chem 266:8647Google Scholar
  9. 9.
    Duronio RJ, Reed SI, Gordon JI (1992) Mutations of human myristoyl-CoA:protein N-myristoyltransferase cause temperature-sensitive myristic acid auxotrophy in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 89:4129. doi: 10.1073/pnas.89.9.4129 CrossRefGoogle Scholar
  10. 10.
    Giang DK, Cravatt BF (1998) A second mammalian N-myristoyltransferase. J Biol Chem 273:6595. doi: 10.1074/jbc.273.12.6595 CrossRefGoogle Scholar
  11. 11.
    Rioux V, Beauchamp E, Pedrono F, Daval S, Molle D, Catheline D, Legrand P (2006) Identification and characterization of recombinant and native rat myristoyl-CoA: protein N-myristoyltransferases. Mol Cell Biochem 286:161. doi: 10.1007/s11010-005-9108-0 CrossRefGoogle Scholar
  12. 12.
    Duronio RJ, Towler DA, Heuckeroth RO, Gordon JI (1989) Disruption of the yeast N-myristoyl transferase gene causes recessive lethality. Science 243:796. doi: 10.1126/science.2644694 CrossRefGoogle Scholar
  13. 13.
    Lodge JK, Jackson-Machelski E, Toffaletti DL, Perfect JR, Gordon JI (1994) Targeted gene replacement demonstrates that myristoyl-CoA: protein N-myristoyltransferase is essential for viability of Cryptococcus neoformans. Proc Natl Acad Sci USA 91:12008. doi: 10.1073/pnas.91.25.12008 CrossRefGoogle Scholar
  14. 14.
    Weinberg RA, McWherter CA, Freeman SK, Wood DC, Gordon JI, Lee SC (1995) Genetic studies reveal that myristoylCoA:protein N-myristoyltransferase is an essential enzyme in Candida albicans. Mol Microbiol 16:241. doi: 10.1111/j.1365-2958.1995.tb02296.x CrossRefGoogle Scholar
  15. 15.
    Gunaratne RS, Sajid M, Ling IT, Tripathi R, Pachebat JA, Holder AA (2000) Characterization of N-myristoyltransferase from Plasmodium falciparum. Biochem J 348:459. doi: 10.1042/0264-6021:3480459 CrossRefGoogle Scholar
  16. 16.
    Price HP, Menon MR, Panethymitaki C, Goulding D, McKean PG, Smith DF (2003) Myristoyl-CoA:protein N-myristoyltransferase, an essential enzyme and potential drug target in kinetoplastid parasites. J Biol Chem 278:7206. doi: 10.1074/jbc.M211391200 CrossRefGoogle Scholar
  17. 17.
    Selvakumar P, Lakshmikuttyamma A, Shrivastav A, Das SB, Dimmock JR, Sharma RK (2007) Potential role of N-myristoyltransferase in cancer. Prog Lipid Res 46:1. doi: 10.1016/j.plipres.2006.05.002 CrossRefGoogle Scholar
  18. 18.
    Hill BT, Skowronski J (2005) Human N-myristoyltransferases form stable complexes with lentiviral nef and other viral and cellular substrate proteins. J Virol 79:1133. doi: 10.1128/JVI.79.2.1133-1141.2005 CrossRefGoogle Scholar
  19. 19.
    Georgopapadakou NH (2002) Antifungals targeted to protein modification: focus on protein N-myristoyltransferase. Expert Opin Investig Drugs 11:1117. doi: 10.1517/13543784.11.8.1117 CrossRefGoogle Scholar
  20. 20.
    Bhatnagar RS, Futterer K, Farazi TA, Korolev S, Murray CL, Jackson-Machelski E, Gokel GW, Gordon JI, Waksman G (1998) Structure of N-myristoyltransferase with bound myristoylCoA and peptide substrate analogs. Nat Struct Biol 5:1091. doi: 10.1038/4202 CrossRefGoogle Scholar
  21. 21.
    Farazi TA, Waksman G, Gordon JI (2001) Structures of Saccharomyces cerevisiae N-myristoyltransferase with bound myristoylCoA and peptide provide insights about substrate recognition and catalysis. Biochemistry 40:6335. doi: 10.1021/bi0101401 CrossRefGoogle Scholar
  22. 22.
    Sogabe S, Masubuchi M, Sakata K, Fukami TA, Morikami K, Shiratori Y, Ebiike H, Kawasaki K, Aoki Y, Shimma N, D’Arcy A, Winkler FK, Banner DW, Ohtsuka T (2002) Crystal structures of Candida albicans N-myristoyltransferase with two distinct inhibitors. Chem Biol 9:1119. doi: 10.1016/S1074-5521(02)00240-5 CrossRefGoogle Scholar
  23. 23.
    Weston SA, Camble R, Colls J, Rosenbrock G, Taylor I, Egerton M, Tucker AD, Tunnicliffe A, Mistry A, Mancia F, de la Fortelle E, Irwin J, Bricogne G, Pauptit RA (1998) Crystal structure of the anti-fungal target N-myristoyl transferase. Nat Struct Biol 5:213. doi: 10.1038/nsb0398-213 CrossRefGoogle Scholar
  24. 24.
    Wu J, Tao Y, Zhang M, Howard MH, Gutteridge S, Ding J (2007) Crystal structures of Saccharomyces cerevisiae N-myristoyltransferase with bound myristoyl-CoA and inhibitors reveal the functional roles of the N-terminal region. J Biol Chem 282:22185. doi: 10.1074/jbc.M702696200 CrossRefGoogle Scholar
  25. 25.
    Ebiike H, Masubuchi M, Liu P, Kawasaki K, Morikami K, Sogabe S, Hayase M, Fujii T, Sakata K, Shindoh H, Shiratori Y, Aoki Y, Ohtsuka T, Shimma N (2002) Design and synthesis of novel benzofurans as a new class of antifungal agents targeting fungal N-myristoyltransferase. Part 2. Bioorg Med Chem Lett 12:607. doi: 10.1016/S0960-894X(01)00808-3 CrossRefGoogle Scholar
  26. 26.
    Kawasaki K, Masubuchi M, Morikami K, Sogabe S, Aoyama T, Ebiike H, Niizuma S, Hayase M, Fujii T, Sakata K, Shindoh H, Shiratori Y, Aoki Y, Ohtsuka T, Shimma N (2003) Design and synthesis of novel benzofurans as a new class of antifungal agents targeting fungal N-myristoyltransferase. Part 3. Bioorg Med Chem Lett 13:87. doi: 10.1016/S0960-894X(02)00844-2 CrossRefGoogle Scholar
  27. 27.
    Masubuchi M, Ebiike H, Kawasaki K, Sogabe S, Morikami K, Shiratori Y, Tsujii S, Fujii T, Sakata K, Hayase M, Shindoh H, Aoki Y, Ohtsuka T, Shimma N (2003) Synthesis and biological activities of benzofuran antifungal agents targeting fungal N-myristoyltransferase. Bioorg Med Chem 11:4463. doi: 10.1016/S0968-0896(03)00429-2 CrossRefGoogle Scholar
  28. 28.
    Masubuchi M, Kawasaki K, Ebiike H, Ikeda Y, Tsujii S, Sogabe S, Fujii T, Sakata K, Shiratori Y, Aoki Y, Ohtsuka T, Shimma N (2001) Design and synthesis of novel benzofurans as a new class of antifungal agents targeting fungal N-myristoyltransferase. Part 1. Bioorg Med Chem Lett 11:1833. doi: 10.1016/S0960-894X(01)00319-5 CrossRefGoogle Scholar
  29. 29.
    Ebara S, Naito H, Nakazawa K, Ishii F, Nakamura M (2005) FTR1335 is a novel synthetic inhibitor of Candida albicans N-myristoyltransferase with fungicidal activity. Biol Pharm Bull 28:591. doi: 10.1248/bpb.28.591 CrossRefGoogle Scholar
  30. 30.
    Yamazaki K, Kaneko Y, Suwa K, Ebara S, Nakazawa K, Yasuno K (2005) Synthesis of potent and selective inhibitors of Candida albicans N-myristoyltransferase based on the benzothiazole structure. Bioorg Med Chem 13:2509. doi: 10.1016/j.bmc.2005.01.033 CrossRefGoogle Scholar
  31. 31.
    Renslo AR, McKerrow JH (2006) Drug discovery and development for neglected parasitic diseases. Nat Chem Biol 2:701. doi: 10.1038/nchembio837 CrossRefGoogle Scholar
  32. 32.
    Bowyer PW, Tate EW, Leatherbarrow RJ, Holder AA, Smith DF, Brown KA (2008) N-Myristoyltransferase: a prospective drug target for protozoan parasites. ChemMedChem 3:402. doi: 10.1002/cmdc.200700301 CrossRefGoogle Scholar
  33. 33.
    Panethymitaki C, Bowyer PW, Price HP, Leatherbarrow RJ, Brown KA, Smith DF (2006) Characterization and selective inhibition of myristoyl-CoA:protein N-myristoyltransferase from Trypanosoma brucei and Leishmania major. Biochem J 396:277. doi: 10.1042/BJ20051886 CrossRefGoogle Scholar
  34. 34.
    Bowyer PW, Gunaratne RS, Grainger M, Withers-Martinez C, Wickramsinghe SR, Tate EW, Leatherbarrow RJ, Brown KA, Holder AA, Smith DF (2007) Molecules incorporating a benzothiazole core scaffold inhibit the N-myristoyltransferase of Plasmodium falciparum. Biochem J 408:173. doi: 10.1042/BJ20070692 CrossRefGoogle Scholar
  35. 35.
    Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 26:283. doi: 10.1107/S0021889892009944 CrossRefGoogle Scholar
  36. 36.
    Luthy R, Bowie JU, Eisenberg D (1992) Assessment of protein models with three-dimensional profiles. Nature 356:83. doi: 10.1038/356083a0 CrossRefGoogle Scholar
  37. 37.
    Miranker A, Karplus M (1991) Functionality maps of binding sites: a multiple copy simultaneous search method. Proteins 11:29. doi: 10.1002/prot.340110104 CrossRefGoogle Scholar
  38. 38.
    Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577. doi: 10.1002/bip.360221211 CrossRefGoogle Scholar
  39. 39.
    Evensen E, Joseph-McCarthy D, Weiss GA, Schreiber SL, Karplus M (2007) Ligand design by a combinatorial approach based on modeling and experiment: application to HLA-DR4. J Comput Aided Mol Des 21:395. doi: 10.1007/s10822-007-9119-x CrossRefGoogle Scholar
  40. 40.
    Sheng C, Zhu J, Zhang W, Zhang M, Ji H, Song Y, Xu H, Yao J, Miao Z, Zhou Y, Lu J (2007) 3D-QSAR and molecular docking studies on benzothiazole derivatives as Candida albicans N-myristoyltransferase inhibitors. Eur J Med Chem 42:477. doi: 10.1016/j.ejmech.2006.11.001 CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  • Chunquan Sheng
    • 1
  • Haitao Ji
    • 2
    • 3
    • 4
  • Zhenyuan Miao
    • 1
  • Xiaoyin Che
    • 1
  • Jianzhong Yao
    • 1
  • Wenya Wang
    • 1
  • Guoqiang Dong
    • 1
  • Wei Guo
    • 1
  • Jiaguo Lü
    • 1
  • Wannian Zhang
    • 1
  1. 1.School of Pharmacy, Military Key Laboratory of Medicinal ChemistrySecond Military Medical UniversityShanghaiPeople’s Republic of China
  2. 2.Department of ChemistryNorthwestern UniversityEvanstonUSA
  3. 3.Department of Biochemistry, Molecular Biology, and Cell BiologyNorthwestern UniversityEvanstonUSA
  4. 4.Center for Drug Discovery and Chemical BiologyNorthwestern UniversityEvanstonUSA

Personalised recommendations