Identification of novel molecular scaffolds for the design of MMP-13 inhibitors through Virtual Screening Methods
La Pietra, Valeria (2010) Identification of novel molecular scaffolds for the design of MMP-13 inhibitors through Virtual Screening Methods. [Tesi di dottorato] (Inedito)
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Osteoarthritis (OA) is the leading cause of joint pain and disability in middle-aged and elderly patients. It is characterized by progressive loss of articular cartilage that eventually leads to denudation of the joint surface. The cartilage loss observed in OA is the result of a complex process involving degradation of various components of the cartilage matrix. Particularly, degradation of cartilage-specific type II collagen by mammalian collagenases (MMPs) is a key step in the loss of structural and functional integrity of cartilage.1 Among all known MMPs, MMP-13 is considered the principal target in OA. Indeed, today there are overwhelming data on the role of MMP-13 in the pathogenesis of OA,2 and inhibition of its activity has proven to be efficacious in a variety of models of experimentally induced as well as spontaneously occurring OA.3 Unfortunately, none of the known MMP inhibitors (MMPIs) have been successfully utilized as therapeutic agents so far. This was due to the lack of selectivity for a specific isozyme, leading to heavy dose- and durationdependent musculoskeletal side effects.4 Therefore, current drug development strategies for treatment of OA are focused on selective inhibition of MMP-13, although recent evidences suggest that other MMPs, such as MMP-1, may also contribute to the collagen degradation process.5 However, the design of a selective MMPI is not a trivial task, as Pag. 7 MMPs share an high similarity in the overall three-dimensional fold and many conserved amino acids exist in the inhibitor binding site, besides the conserved catalytic zinc ion. The major structural difference observed between the MMP enzymes resides in the relative size and shape of the S1’ subsite, which is located in proximity of the catalytic metal. From a structural point of view, almost all MMPIs known so far are based on a zinc-binding group (ZBG) and a hydrophobic portion protruding into the hydrophobic S1’ subsite. These compounds behave as competitive inhibitors since the ZBG can mimic one of the transition states occurring during the substrate hydrolysis. Currently, two successful strategies to confer selectivity of action to an MMP inhibitor are known: the first resides in the proper modification of the P1’ substituent on MMPI to take advantage of the differences between the diverse MMPs; the second is the finding of an allosteric inhibitor,6 which binds tightly to the S1’ and S1’* subsite without chelating the metal that is thought to contribute to the promiscuous inhibition of multiple MMPs.Errore. Il segnalibro non è definito.c Recently, as a result of the first strategy, it has been designed a Nisopropoxy- arylsulfonamide-based hydroxamate inhibitor, which showed low nanomolar activity for MMP-13 and high selectivity over some other tested MMPs.7 In parallel to further studies aiming to assess the activity of this promising compound using in vivo models of OA, it has been decided to seek for novel scaffolds as allosteric inhibitors on one hand, and as zincchelating non-hydroxamate inhibitors on the other. In fact, a debate is still open on the advisability of using hydroxamates as ZBG due to toxicity and metabolic stability issues.8,9 In this respect, we have taken advantage of the availability of several MMP-13 crystal structures and have used two different in silico methods to screen the Life Chemicals and the Maybridge databases, respectively. Experimental tests of a limited selection of candidate compounds (60) verified nine novel leads, structurally unrelated to the known MMPIs.
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