Abstract
The anticancer drug 1843U89 inhibits thymidylate synthase (TS) at sub-nanomolar concentrations and is undergoing clinical trial. The 1.95 Å crystal structure of Escherichia coli TS bound to the drug and dUMP reveals that the 1843U89 binding surface includes a hydrophobic patch that is normally buried. To reach this patch, 1843U89 inserts into the wall of the TS active site, resulting in a severe local distortion of the protein. In this new conformation, active-site groups that normally bind to the catalytic cofactor methylene-tetrahydrofolate instead bind to 1843U89 in new ways. This structure provides a rare example of a protein that can bind tightly to distinct substances using a single, flexible, binding surface. This has implications for drug design, as 1843U89 could not have been obtained from current structure-based approaches.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$189.00 per year
only $15.75 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Santi, D.V. & Danenberg, P.V. in Folates and Pterins: Volume 1 -Chemistry and Biochemistry of Folates (eds Blakley, R.L. & Benkovic, S.J.) 345–398 (John Wiley & Sons, Inc., New York, 1984).
Dev, I.K. et al. Mode of binding of folate analogs to thymidylate synthase. J. biol. Chem. 269, 1873–1882 (1994).
Duch, D.S. et al. Biochemical and cellular pharmacology of 1843U89, a novel benzoquinazoline inhibitor of thymidylate synthase. Cancer Res. 53, 810–818 (1993).
Jones, T.R. et al. A potent antitumor quinazoline inhibitor of thymidylate synthetase: synthesis, biological properties, and therapeutic results in mice. Eur. J. Cancer 17, 11–19 (1981).
Alison, D.L. et al. The clinical pharmacokinetics of the novel antifolate N10-propargyl-5,8-dideazafolic acid (CB3717). Cancer chemother. Pharmacol. 14, 265–271 (1985).
Montfort, W.R. et al. Structure, multiple site binding, and segmental accomodation in thymidylate synthase on binding dUMP and an anti-folate. Biochemistry 29, 6964–6977 (1990).
Matthews, D.A., Appelt, K., Oatley, S.J. & Xuong, N.H. Crystal structure of Escherichia coli thymidylate synthase containing bound 5-fluoro-2′-deoxyuridylate and 10-propargyl-5,8-dideazafolate. J. molec. Biol. 214, 923–936 (1990).
Matthews, D.A. et al. Stereochemical mechanism of action for thymidylate synthase based on the X-ray structure of the covalent inhibitor ternary complex with 5-fluoro-2′-deoxyuridylate and 5,10-methylenetetrahydrofolate. J. molec. Biol. 214, 937–948 (1990).
Finer-Moore, J.S., Montfort, W.R. & Stroud, R.M. Pairwise specificity and sequential binding in enzyme catalysis: thymidylate synthase. Biochemistry 29, 6977–6986 (1990).
Fauman, E.B., Rutenber, E.E., Maley, G.F., Maley, F. & Stroud, R.M. Water-mediated substrate/product discrimination: the product complex of thymidylate synthase at 1.83 Å. Biochemistry 33, 1502–1511 (1994).
Weichsel, A., Montfort, W.R., Ciesla, J. & Maley, F. Promotion of purine nucleotide binding to thymidylate synthase by a potent folate analogue inhibitor, 1843U89. Proc. natn. Acad. Sci. U.S.A. 92, 3493–3497 (1995).
Perry, K.M. et al. Plastic adaptation toward mutations in proteins: structural comparison of thymidylate synthases. Proteins Struct. Funct. Genet. 8, 315–333 (1990).
Maley, G.F., Maley, F. & Baugh, C.M. Studies on identifying the folylpolyglutamate binding sites of Lactobacillus casei thymidylate synthetase. Arch. Biochem. Biophys. 216, 551–558 (1982).
Kamb, A., Finer-Moore, J., Calvert, A.H. & Stroud, R.M. Structural basis for recognition of polyglutamyl folates by thymidylate synthase. Biochemistry 31, 9883–9890 (1992).
Hughes, L.R. et al. Quinazoline antifolate thymidylate synthase inhibitors: alkyl, substituted alkyl, and aryl substituents in C2 position. J. med. Chem. 33, 3060–3067 (1990).
Appelt, K. et al. Design of enzyme inhibitors using iterative protein crystallographic analysis. J. med. Chem. 34, 1925–1934 (1991).
Bystroff, C. & Kraut, J. Crystal structure of unliganded Escherichia coli dihydrofolate reductase. Ligand-induced conformational changes and cooperativity in binding. Biochemistry 30, 2227–2239 (1991).
Bolin, J.T., Filman, D.J., Matthews, D.A., Hamlin, R.C. & Kraut, J. Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 Å resolution. J. biol. Chem. 257, 13650–13662 (1982).
DeVos, A.M., Ultsch, M. & Kossiakoff, A.A. Human growth hormone and extracellular domain of its receptor: crystal structure of the complex. Science 255, 306–312 (1992).
Fenton, W.A., Kashi, Y., Furtak, K. & Horwich, A.L. Residues in chaperonin GroEL required for polypeptide binding and release. Nature 371, 614–619 (1994).
Braig, K. et al. The crystal structure of the bacterial chaperonin GroEL at 2.8 Å. Nature 371, 578–586 (1994).
Shoichet, B.K., Stroud, R.M., Santi, D.V., Kuntz, I.D. & Perry, K.M. Structure-based discovery of inhibitors of thymidylate synthase. Science 259, 1445–1450 (1993).
Verlinde, C.L. & Hol, W.G. Structure-based drug design: progress, results and challenges. Structure 2, 577–587 (1994).
Maley, G.F. & Maley, F. Properties of a defined mutant of Escherichia coli thymidylate synthase. J. biol. Chem. 263, 7620–7627 (1988).
Messerschmidt, A. & Pflugrath, J.W. Crystal orientation and X-ray pattern prediction routines for area-detector diffractometer systems in macromolecular crystallography. J. appl. Crystallogr. 20, 306–315 (1987).
Kabsch, W. Evaluation of single-crystal X-ray diffraction data from a position-sensitive detector. J. appl. Crystallogr. 21, 916–934 (1988).
Weissman, L. Strategies for extracting isomorphous and anomalous signals in Computational Crystallography (ed Sayre, D.) 56–63 (Clarendon Press, Oxford, 1982).
Colloborative computational project, Number 4. The CCP4 Suite: Programs for Protein Crystallography. Acta Crystallogr. D50, 760–763 (1994).
Pflugrath, J.W., Saper, M.A. & Quiocho, F.A. New generation graphics system for macromolecular modeling. Methods and Applications in Crystallographic Computing (eds Hall, S. & Ashida, T.) 404–407 (Clarendon Press, Oxford, 1984).
Jones, A. A Graphics Model Building and Refinement System for Macromolecules. J. appl. Crystallogr. 11, 268–272 (1978).
Insight-II User Guide version 2.2.0 San Diego: Biosym Technologies. (1993).
Furey, W., Wang, B.C. & Sax, M. Crystallographic computing on an array processor. J. appl. Crystallogr. 15, 160–166 (1982).
Hendrickson, W. Stereochemically restrained refinement of macromolecular structures. Meth. Enzymol. 115, 252–270 (1985).
Nichols, A., Bharadwaj, R. & Honig, B. GRASP–graphical representation and analysis of surface properties. Biophys. J. 64, A166 (1993).
Carson, M. Ribbon models of macromolecules. J. molec. Graph. 5, 103–106 (1987).
Kraulis, P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. appl. Crystallogr. 24, 946–950 (1991).
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Weichsel, A., Montfort, W. Ligand-induced distortion of an active site in thymidylate synthase upon binding anticancerdrug 1843U89. Nat Struct Mol Biol 2, 1095–1101 (1995). https://doi.org/10.1038/nsb1295-1095
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1038/nsb1295-1095
This article is cited by
-
Molecular recognition phenomenon in aromatic compounds
Research on Chemical Intermediates (2013)
-
Implications of protein flexibility for drug discovery
Nature Reviews Drug Discovery (2003)