Structure-based discovery and in-parallel optimization of novel competitive inhibitors of thymidylate synthase

Donatella Tondi, Ursula Slomczynska, M. Paola Costi, D. Martin Watterson, Stefano Ghelli, Brian K. Shoichet*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

67 Scopus citations


Background: The substrate sites of enzymes are attractive targets for structure-based inhibitor design. Two difficulties hinder efforts to discover and elaborate new (nonsubstrate-like) inhibitors for these sites. First, novel inhibitors often bind at nonsubstrate sites. Second, a novel scaffold introduces chemistry that is frequently unfamiliar, making synthetic elaboration challenging. Results: In an effort to discover and elaborate a novel scaffold for a substrate site, we combined structure-based screening with in-parallel synthetic elaboration. These techniques were used to find new inhibitors that bound to the folate site of Lactobacillus casei thymidylate synthase (LcTS), an enzyme that is a potential target for proliferative diseases, and is highly studied. The available chemicals directory was screened, using a molecular-docking computer program, for molecules that complemented the three-dimensional structure of this site. Five high-ranking compounds were selected for testing. Activity and docking studies led to a derivative of one of these, dansyltyrosine (K(i) 65 μM). Using solid-phase in-parallel techniques 33 derivatives of this lead were synthesized and tested. These analogs are dissimilar to the substrate but bind competitively with it. The most active analog had a K(i) of 1.3 μM. The tighter binding inhibitors were also the most specific for LcTS versus related enzymes. Conclusions: TS can recognize inhibitors that are dissimilar to, but that bind competitively with, the folate substrate. Combining structure-based discovery with in-parallel synthetic techniques allowed the rapid elaboration of this series of compounds. More automated versions of this approach can be envisaged.

Original languageEnglish (US)
Pages (from-to)319-331
Number of pages13
JournalChemistry and Biology
Issue number5
StatePublished - May 1999


  • Computer-based inhibitor design
  • Enzyme specificity
  • In-parallel synthesis
  • Structure-based drug design

ASJC Scopus subject areas

  • Drug Discovery
  • Molecular Medicine
  • Molecular Biology
  • Biochemistry
  • Clinical Biochemistry
  • Pharmacology


Dive into the research topics of 'Structure-based discovery and in-parallel optimization of novel competitive inhibitors of thymidylate synthase'. Together they form a unique fingerprint.

Cite this