Chemistry & Biology
Volume 6, Issue 5, May 1999, Pages 319-331
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Structure-based discovery and in-parallel optimization of novelcompetitive inhibitors of thymidylate synthase

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Abstract

Background:

The substrate sites of enzymes are attractive targets for structurebased 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 clocking studies led to a derivative of one of these, dansyltyrosine (Ki 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 Ki 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.

Key words

computer-based inhibitor design
enzymespecificity
in-parallel synthesis
structure-based drug design

Cited by (0)

Present addresses: Dipartimento di Scienze Farmaceutiche, Università degli Studi di Modena, 183 Via Campi, Modena, Italy.

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MetaPhorePharmaceuticals Inc., 3655 Vista Avenue, St. Louis, MO 63110, USA.