ARTICLE pubs.acs.org/jmc Structure-Based Design of Novel Boronic Acid-Based Inhibitors of Autotaxin Harald M. H. G. Albers,‡,§ Loes J. D. Hendrickx,‡,† Rob J. P. van Tol,‡ Jens Hausmann,r Anastassis Perrakis,r and Huib Ovaa*,‡,§ ‡Division of Cell Biology, §Netherlands Proteomics Centre, and rDivision of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands bS Supporting Information ABSTRACT: Autotaxin (ATX) is a secreted phosphodiesterase that hydrolyzes the abundant phospholipid lysophosphatidylcholine (LPC) to produce lysopho- sphatidic acid (LPA). The ATX-LPA signaling axis has been implicated in inﬂammation, ﬁbrosis, and tumor progression, rendering ATX an attractive drug target. We recently described a boronic acid-based inhibitor of ATX, named HA155 (1). Here, we report the design of new inhibitors based on the crystal structure of ATX in complex with inhibitor 1. Furthermore, we describe the syntheses and activities of these new inhibitors, whose potencies can be explained by structural data. To understand the diﬀerence in activity between two diﬀerent isomers with nanomolar potencies, we performed molecular docking experiments. Intriguingly, molecular docking suggested a remarkable binding pose for one of the isomers, which diﬀers from the original binding pose of inhibitor 1 for ATX, opening further options for inhibitor design. ’ INTRODUCTION The secreted glycoprotein autotaxin (ATX) is a phosphodies- terase responsible for the hydrolysis of lysophosphatidylcholine (LPC) into lysophosphatidic acid (LPA) and choline, as depicted in Scheme 1.1,2 The bioactive lipid LPA stimulates migration, proliferation and survival of cells by activating speciﬁc G protein- coupled receptors.3 The ATX-LPA signaling axis is involved in cancer, inﬂammation and ﬁbrotic disease.4 6 Potent and selec- tive ATX inhibitors are needed to elucidate the contribution of ATX action to signaling cascades that may result in disease in case of malfunction. ATX, also known as eNPP2, is a unique member of the ecto- nucleotide pyrophosphatase/phosphodiesterase (eNPP) family of proteins. It is the only family member capable of producing LPA by hydrolysis of LPC.7 Recently reported crystal structures of mouse8 and rat9 ATX conﬁrmed that a threonine residue and two zinc ions are necessary for activity of ATX.10 From these structures, it could be concluded that ATX hydrolyzes its sub- strates through a typical alkaline phosphatase/phosphodiesterase mechanism.11,12 Furthermore, these structures showed that ATX speciﬁcally binds its lipid substrates in a hydrophobic pocket extending from the active site of ATX. This pocket accommo- dates the alkyl chain of the lipids in diﬀerent poses as was also shown in various crystal structures.8 Recently, we described the discovery of a boronic acid-based ATX inhibitors that helped to reveal the short half-life (∼5 min) of LPA in vivo.13,14 We introduced a boronic acid moiety in the inhibitor structure to rationally target the threonine oxygen nucleophile of ATX with a hard matching Lewis acid. The crystal structure of ATX in complex with HA155 (1)9 conﬁrmed our hypothesis that this inhibitor targets the threonine oxygen nucleophile in the ATX active site via the boronic acid moiety, while the hydrophobic 4-ﬂuorobenzyl moiety of inhibitor 1 targets the hydrophobic pocket responsible for lipid binding (Figure 1). Here, we report a number of synthetic routes, systematically substituting linkers and the thiazolidine-2,4-dione core in 1, while keeping the boronic acid moiety untouched. The observed structure activity relations could well be explained from the ATX structure in complex with inhibitor 1. A remarkable binding pose of a novel inhibitor, as predicted from molecular docking experiments, suggests additional avenues for further inhibitor design. ’ RESULTS AND DISCUSSION Design of Inhibitors. The structure of inhibitor 1 bound to the ATX active site (Figure 1) showed that its 4-fluorobenzyl moiety binds into the hydrophobic lipid binding pocket of ATX (Figure 1C,D).9 This pocket also accommodates the lipid tail of LPA, the hydrolysis product of LPC.8 The thiazolidine-2,4-dione core of 1 and the conjugated aromatic ring are located between the hydrophobic pocket and the catalytic site (Figure 1D). The ether linker, bridging the two aromatic rings in 1, and especially a Received: Published: March 18, 2011 May 26, 2011 r 2011 American Chemical Society 4619 dx.doi.org/10.1021/jm200310q | J. Med. Chem. 2011, 54, 4619–4626