Investigational New Drugs

, Volume 31, Issue 5, pp 1355–1363 | Cite as

In silico analysis of the amido phosphoribosyltransferase inhibition by PY873, PY899 and a derivative of isophthalic acid

  • Sidra Batool
  • Muhammad Sulaman Nawaz
  • Mohammad A. KamalEmail author


Selectively decreasing the availability of precursors for the de novo biosynthesis of purine nucleotides is a valid approach towards seeking a cure for leukaemia. Nucleotides and deoxynucleotides are required by living cells for syntheses of RNA, DNA, and cofactors such as NADP+, FAD+, coenzyme A and ATP. Nucleotides contain purine and pyrimidine bases, which can be synthesized through salvage pathway as well. Amido phosphoribosyltransferase (APRT), also known as glutamine phosphoribosylpyrophosphate amidotransferase (GPAT), is an enzyme that in humans is encoded by the PPAT (phosphoribosyl pyrophosphate amidotransferase) gene. APRT catalyzes the first committed step of the de novo pathway using its substrate, phosphoribosyl pyrophosphate (PRPP). As APRT is inhibited by many folate analogues, therefore, in this study we focused on the inhibitory effects of three folate analogues on APRT activity. This is extension of our previous wet lab work to analyze and dissect molecular interaction and inhibition mechanism using molecular modeling and docking tools in the current study. Comparative molecular docking studies were carried out for three diamino folate derivatives employing a model of the human enzyme that was built using the 3D structure of Bacillus subtilis APRT (PDB ID; 1GPH) as the template. Binding orientation of interactome indicates that all compounds having nominal cluster RMSD in same active site’s deep narrow polar fissure. On the basis of comparative conformational analysis, electrostatic interaction, binding free energy and binding orientation of interactome, we support the possibility that these molecules could behave as APRT inhibitors and therefore may block purine de novo biosynthesis. Consequently, we suggest that PY899 is the most active biological compound that would be a more potent inhibitor for APRT inhibition than PY873 and DIA, which also confirms previous wet lab report.


Amido phosphoribosyltransferase In silico Inhibition PY873 PY899 Isophthalic acid 



Amido phosphoribosyltransferase


5-((4-carboxy-4-(4-(((2,4-diaminopyrido[3,2-d]pyrimidine-6-yl)methyl)amino)benzamido)butyl)carbamoyl)isophthalic acid


Dihydrofolate reductase






Phosphoribosyl pyrophosphate





Authors are grateful to Prof. F. Gago, (Department of Pharmacology, School of Medicine, University of Alcala, E-28871 Alcala de Henares, Madrid, Spain) for his help in some editing and valuable comments to improve the quality of this manuscript. Authors are also thankful to Ms. Zunaira Asif for assisting in drawing of figure 1 (schematic representation of de novo and salvage pathway).

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

10637_2013_9944_MOESM1_ESM.pdf (165 kb)
Suppl. Figure 1 (a) 3D structure of target, (b) 3D structure of template, (c) target and template superimposition (PDF 165 kb)


  1. 1.
    Kamal MA, Christopherson RI (2004) Accumulation of 5-phosphoribosyl-1-pyrophosphate in human CCRF-CEM leukaemia cells treated with antifolates. Int J Biochem Cell Biol 36:545–551CrossRefGoogle Scholar
  2. 2.
    Wood AW, Seegmiller JE (1973) Properties of 5-phosphoribosyl-1-pyrophosphate amidotransferase from human lymphoblasts. J Biol Chem 248:138–143PubMedGoogle Scholar
  3. 3.
    Schendel FJ, Cheng YS, Otvos JD, Wehrli S, Stubbe J (1988) Characterization and chemical properties of phosphoribosylamine, an unstable intermediate in the de novo purine biosynthetic pathway. Biochemistry 27:2614–2623CrossRefGoogle Scholar
  4. 4.
    Sant ME, Lyons SD, Phillips L, Christopherson RI (1992) Antifolates induce inhibition of amido phosphoribosyltransferase in leukemia cells. J Biol Chem 267:11038–11045PubMedGoogle Scholar
  5. 5.
    Schoettle SL, Crisp LB, Szabados E, Christopherson RI (1997) Mechanisms of inhibition of amido phosphoribosyltransferase from mouse L1210 leukemia cells. Biochemistry 36:6377–6383CrossRefGoogle Scholar
  6. 6.
    Rosowsky A, Galivan J, Beardsley GP, Bader H, O’Connor BM, Russello O, Moroson BA, DeYarman MT, Kerwar SS, Freisheim JH (1992) Biochemical and biological studies on 2-desamino-2-methylaminopterin, an antifolate the polyglutamates of which are more potent than the monoglutamate against three key enzymes of folate metabolism. Cancer Res 52:2148–2155PubMedGoogle Scholar
  7. 7.
    Nayeem A, Sitkoff D, Krystek S Jr (2006) A comparative study of available software for high-accuracy homology modeling: from sequence alignments to structural models. Protein Sci 15:808–824CrossRefGoogle Scholar
  8. 8.
    Tramontano A (1998) Homology modeling with low sequence identity. Methods 14:293–300CrossRefGoogle Scholar
  9. 9.
    Schwede T, Kopp J, Guex N, Peitsch MC (2003) SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res 31:3381–3385CrossRefGoogle Scholar
  10. 10.
    Peitsch MC (1996) ProMod and Swiss-Model: internet-based tools for automated comparative protein modelling. Biochem Soc Trans 24:274–279CrossRefGoogle Scholar
  11. 11.
    Christen M, Hunenberger PH, Bakowies D, Baron R, Burgi R, Geerke DP, Heinz TN, Kastenholz MA, Krautler V, Oostenbrink C, Peter C, Trzesniak D, van Gunsteren WF (2005) The GROMOS software for biomolecular simulation: GROMOS05. J Comput Chem 26:1719–1751CrossRefGoogle Scholar
  12. 12.
    Gopalakrishnan K, Sowmiya G, Sheik SS, Sekar K. Ramachandran plot on the Web (2.0), Protein Pept Lett 669–671(3)Google Scholar
  13. 13.
    Laskowski RA, Rullmannn JA, MacArthur MW, Kaptein R, Thornton JM (1996) AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 8:477–486CrossRefGoogle Scholar
  14. 14.
    Colovos C, Yeates TO (1993) Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci 2:1511–1519CrossRefGoogle Scholar
  15. 15.
    Vriend G, Sander C (1993) Quality control of protein models: directional atomic contact analysis. J Appl Crystallogr 26:47–60CrossRefGoogle Scholar
  16. 16.
    CambridgeSoft Corporation: Chemoffice (2010), USAGoogle Scholar
  17. 17.
    James JP, Stewart (2008) MOPAC2009, Stewart Computational Chemistry, Colorado Springs, CO, USA,
  18. 18.
    Rosowsky A, Papoulis AT, Forsch RA, Queener SF (1999) Synthesis and antiparasitic and antitumor activity of 2, 4-diamino-6-(arylmethyl)-5,6,7,8-tetrahydroquinazoline analogues of piritrexim. J Med Chem 42:1007–1017CrossRefGoogle Scholar
  19. 19.
    Gangjee A, Yang J, McGuire JJ, Kisliuk RL (2006) Synthesis and evaluation of a classical 2,4-diamino-5-substituted-furo[2,3-d]pyrimidine and a 2-amino-4-oxo-6-substituted-pyrrolo[2,3-d]pyrimidine as antifolates. Bioorg Med Chem 14:8590–8598CrossRefGoogle Scholar
  20. 20.
    Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ (1998) Automated docking using a lamarckian genetic algorithm and empirical binding free energy function. J Comput Chem 19:1639–1662CrossRefGoogle Scholar
  21. 21.
    Smith JL, Zaluzec EJ, Wery JP, Niu L, Switzer RL, Zalkin H, Satow Y (1994) Structure of the allosteric regulatory enzyme of purine biosynthesis. Science 264:1427–1433CrossRefGoogle Scholar
  22. 22.
    Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF Chimera–a visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612CrossRefGoogle Scholar
  23. 23.
    Baram J, Chabner BA, Drake JC, Fitzhugh AL, Sholar PW, Allegra CJ (1988) Identification and biochemical properties of 10-formyldihydrofolate, a novel folate found in methotrexate-treated cells. J Biol Chem 263:7105–7111PubMedGoogle Scholar
  24. 24.
    Allegra CJ, Chabner BA, Drake JC, Lutz R, Rodbard D, Jolivet J (1985) Enhanced inhibition of thymidylate synthase by methotrexate polyglutamates. J Biol Chem 260:9720–9726PubMedGoogle Scholar
  25. 25.
    Allegra CJ, Drake JC, Jolivet J, Chabner BA (1985) Inhibition of phosphoribosylaminoimidazolecarboxamide transformylase by methotrexate and dihydrofolic acid polyglutamates. Proc Natl Acad Sci U S A 82:4881–4885CrossRefGoogle Scholar
  26. 26.
    Baggott JE, Vaughn WH, Hudson BB (1986) Inhibition of 5-aminoimidazole-4-carboxamide ribotide transformylase, adenosine deaminase and 5′-adenylate deaminase by polyglutamates of methotrexate and oxidized folates and by 5-aminoimidazole-4-carboxamide riboside and ribotide. Biochem J 236:193–200CrossRefGoogle Scholar
  27. 27.
    Allegra CJ, Fine RL, Drake JC, Chabner BA (1986) The effect of methotrexate on intracellular folate pools in human MCF-7 breast cancer cells. Evidence for direct inhibition of purine synthesis. J Biol Chem 261:6478–6485PubMedGoogle Scholar
  28. 28.
    Baram J, Allegra CJ, Fine RL, Chabner BA (1987) Effect of methotrexate on intracellular folate pools in purified myeloid precursor cells from normal human bone marrow. J Clin Invest 79:692–697CrossRefGoogle Scholar
  29. 29.
    Matherly LH, Barlowe CK, Phillips VM, Goldman ID (1987) The effects on 4-aminoantifolates on 5-formyltetrahydrofolate metabolism in L1210 cells. A biochemical basis of the selectivity of leucovorin rescue. J Biol Chem 262:710–717PubMedGoogle Scholar
  30. 30.
    Zalkin H, Dixon JE (1992) De novo purine nucleotide biosynthesis. Prog Nucleic Acid Res Mol Biol 42:259–287CrossRefGoogle Scholar
  31. 31.
    Gilson MK, Zhou HX (2007) Calculation of protein-ligand binding affinities. Annu Rev Biophys Biomol Struct 36:21–42CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Sidra Batool
    • 1
  • Muhammad Sulaman Nawaz
    • 2
  • Mohammad A. Kamal
    • 3
    Email author
  1. 1.Functional Informatics Laboratory National Center for BioinformaticsQuaid-I-Azam UniversityIslamabadPakistan
  2. 2.Department of BioSciencesCOMSATS Institute of Information TechnologyChak Shahzad IslamabadPakistan
  3. 3.Metabolomics & Enzymology Unit, Fundamental and Applied Biology Group, King Fahd Medical Research CenterKing Abdulaziz UniversityJeddahSaudi Arabia

Personalised recommendations