Future challenges facing the development of specific active-site-directed synthetic inhibitors of MMPs P. Cuniasse a , L. Devel a , A. Makaritis b , F. Beau a , D. Georgiadis b , M. Matziari b , A. Yiotakis b , V. Dive a, * a CEA, Département d’Ingénierie et d’Etudes des Protéines (DIEP), CE-Saclay, 91191 Gif/Yvette cedex, France b Laboratory of Organic Chemistry, Department of Organic Chemistry, University of Athens, Panepistimioplois, Zografou, 15771 Athens Greece Received 21 July 2004; accepted 23 September 2004 Available online 19 October 2004 Abstract Despite a deep knowledge on the 3D-structure of several catalytic domains of MMPs, the development of highly specific synthetic active- site-directed inhibitors of MMPs, able to differentiate the different members of this protease family, remains a strong challenge. Due to the flexible nature of MMP active-site, the development of specific MMP inhibitors will need to combine sophisticated theoretical and experi- mental approaches to decipher in each MMP the specific structural and dynamic features that can be exploited to obtain the desired selectivity. © 2004 Elsevier SAS. All rights reserved. Keywords: MMPs; Inhibitors; Zinc protease; Conformational variability; Inhibitor selectivity 1. Introduction Over the past 20 years, impressive efforts have been dedi- cated to the development of synthetic compounds interacting potently and selectively with the active-site of MMPs [1]. Despite these efforts, inhibitors able to differentiate fully one MMP from the others have not been identified so far. In this review, possible explanations for this situation are discussed, as well as new strategies to develop more selective inhibitors of MMPs. 2. Chemical context MMPs are metalloproteinases characterized by the pres- ence in their active-sites of a catalytically indispensable zinc ion, a property that has been exploited to design synthetic inhibitors of this enzyme family. Thus, the development of synthetic inhibitors of zinc metalloproteinases has relied on the use of a peptide sequence, recognized by the targeted protease, to which have been grafted different chemical func- tionalities able to interact potently with the zinc ion of the active-site. This strategy has allowed the identification of several potent pseudo-peptide inhibitors of MMPs. Based on the chemical structure of the zinc-binding group, four differ- ent classes of zinc metalloprotease inhibitors have been de- veloped, those incorporating a hydroxamate (CONH–O – ), a carboxylate (COO – ), a thiolate (S – ) or a phosphinyl (PO 2 – ) [1]. Interestingly, while only the last three classes of syn- thetic inhibitors have been successfully applied to clinical practice, like those targeting the ACE zinc endopeptidase to combat cardiovascular diseases [2], most of the MMP inhibi- tors produced by pharmaceutical companies belong to the hydroxamate category. This choice was based on early stud- ies showing that extremely potent inhibitors of MMPs can be obtained by grafting a hydroxamate moiety to a suitable peptide sequence (see BB-94 1 ). Also, as no hydroxamate com- pounds were in clinical use at that time, this left many Abbreviations: ACE, angiotensin converting enzyme; ADAM, a disinte- grin and metalloproteinase domain containing protein; MMPs, matrix metal- loproteinase; TACE, tumor necrosis factor-a converting enzyme. * Corresponding author. Tel.: +33-1-69-08-35-85; fax: +33-1-69-08-90-71. E-mail address: vincent.dive@cea.fr (V. Dive). 1 Ki values reported in the text have been determined using synthetic fluo- rogenic substrates. Competitive inhibition for most inhibitors has been demonstrated. Biochimie 87 (2005) 393–402 www.elsevier.com/locate/biochi 0300-9084/$ - see front matter © 2004 Elsevier SAS. All rights reserved. doi:10.1016/j.biochi.2004.09.025