Unraveling Hidden Regulatory Sites in Structurally Homologous Metalloproteases

Udi, Yael; Fragai, Marco; Grossman, Moran; Mitternacht, Simon; Arad‐Yellin, Rina; Calderone, V.; Melikian, Maxime; Toccafondi, Mirco; Berezovsky, Igor N.; Luchinat, Claudio; Sagi, Irit

doi:10.1016/j.jmb.2013.04.009

Cited by 53 publications

(50 citation statements)

References 66 publications

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“…2, 3 and Supplementary Fig. 1) and that overlap at the α-face with binding of a hydrophobic, non-competitive inhibitor 47 . This offers an unprecedented basis to account for the pericellular activity of MMP-12 around activated pulmonary macrophages 14 and HeLa cells (Supplementary Fig.…”

Section: Discussionmentioning

confidence: 99%

Ambidextrous binding of cell and membrane bilayers by soluble matrix metalloproteinase-12

et al. 2014

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Matrix metalloproteinases (MMPs) regulate tissue remodeling, inflammation, and disease progression. Some soluble MMPs are inexplicably active near cell surfaces. Here, we demonstrate binding of MMP-12 directly to bilayers and cellular membranes using paramagnetic NMR and fluorescence. Opposing sides of the catalytic domain engage spin-labeled membrane mimics. Loops project from the β-sheet interface to contact the phospholipid bilayer with basic and hydrophobic residues. The distal membrane interface comprises loops on the other side of the catalytic cleft. Both interfaces mediate MMP-12 association with vesicles and cell membranes. MMP-12 binds plasma membranes and is internalized to hydrophobic perinuclear features, the nuclear membrane, and inside the nucleus within minutes. While binding of TIMP-2 to MMP-12 hinders membrane interactions beside the active site, TIMP-2-inhibited MMP-12 binds vesicles and cells, suggesting compensatory rotation of its membrane approaches. MMP-12 association with diverse cell membranes may target its activities to modulate innate immune responses and inflammation.

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Section: Discussionmentioning

confidence: 99%

Ambidextrous binding of cell and membrane bilayers by soluble matrix metalloproteinase-12

et al. 2014

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“…An alternative approach has targeted the hemopexin domain of membrane type-1 matrix metalloproteinase (MT1-MMP) (14), which is well outside the catalytic domain. In growing efforts to identify inhibitor sites outside of the catalytic domain (15,16), small peptides have been identified that can interfere with the MMP-2 interaction with collagen substrate (17). Although these new approaches hold promise due to enhanced selectivity, the clinical utility of these compounds and others employing alternative inhibitory strategies has not yet been determined.…”

Section: Mmpsmentioning

confidence: 99%

Discovery of a highly selective chemical inhibitor of matrix metalloproteinase-9 (MMP-9) that allosterically inhibits zymogen activation

Scannevin

Alexander

Haarlander

et al. 2017

Journal of Biological Chemistry

114

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Aberrant activation of matrix metalloproteinases (MMPs) is a common feature of pathological cascades observed in diverse disorders, such as cancer, fibrosis, immune dysregulation, and neurodegenerative diseases. MMP-9, in particular, is highly dynamically regulated in several pathological processes. Development of MMP inhibitors has therefore been an attractive strategy for therapeutic intervention. However, a long history of failed clinical trials has demonstrated that broad-spectrum MMP inhibitors have limited clinical utility, which has spurred the development of inhibitors selective for individual MMPs. Attaining selectivity has been technically challenging because of sequence and structural conservation across the various MMPs. Here, through a biochemical and structural screening paradigm, we have identified JNJ0966, a highly selective compound that inhibited activation of MMP-9 zymogen and subsequent generation of catalytically active enzyme. JNJ0966 had no effect on MMP-1, MMP-2, MMP-3, MMP-9, or MMP-14 catalytic activity and did not inhibit activation of the highly related MMP-2 zymogen. The molecular basis for this activity was characterized as an interaction of JNJ0966 with a structural pocket in proximity to the MMP-9 zymogen cleavage site near Arg-106, which is distinct from the catalytic domain. JNJ0966 was efficacious in reducing disease severity in a mouse experimental autoimmune encephalomyelitis model, demonstrating the viability of this therapeutic approach. This discovery reveals an unprecedented pharmacological approach to MMP inhibition, providing an opportunity to improve selectivity of future clinical drug candidates. Targeting zymogen activation in this manner may also allow for pharmaceutical exploration of other enzymes previously viewed as intractable drug targets. MMPs2 are a family of structurally related zinc-binding proteolytic enzymes that digest extracellular matrix proteins and participate in tissue remodeling and signaling events (1). Currently, ϳ23 MMPs have been identified, comprising secreted and membrane-bound forms, and different family members share some common structural and functional domains and have varying degrees of substrate specificity. Abnormal expression and activation of MMPs has been implicated in the pathogenesis and pathological progression of several different human diseases that are centered in many different tissues in the periphery and central nervous system (2, 3). Initial clinical exploration of synthetic MMP inhibitors was focused on oncology indications, as preventing the breakdown of tissue matrices and barriers was viewed as a potential mechanism to limit tumor metastasis.Despite intensive efforts over many years to develop synthetic MMP inhibitors, only a single MMP inhibitor, Periostat, a tetracycline derivative used in periodontal disease, has progressed into regular clinical use (4). Of the ϳ50 other clinical trials conducted with active site MMP inhibitors, all have failed due to the onset of significant dose-limiting musculoskeletal toxicity ...

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“…Oleosins (hydrophobic proteins from seeds) can be kept soluble both by classical APols and by blocky polymers, forming much bigger complexes in the latter case (Gohon et al 2011). Several other studies, which will not be reviewed here, suggest that APols can also be of use for working with non-membrane proteins (Ma et al 2012; Ning et al 2014; Prassl and Laggner 2009; Udi et al 2013; Wolff and Delepierre 1997). …”

Section: Basic Properties Of Amphipols and Membrane Protein/amphipol mentioning

confidence: 99%

Amphipols for Each Season

2014

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Amphipols (APols) are short amphipathic polymers that can substitute for detergents at the transmembrane surface of membrane proteins (MPs) and, thereby, keep them soluble in detergent-free aqueous solutions. APol-trapped MPs are, as a rule, more stable biochemically than their detergent-solubilized counterparts. APols have proven useful to produce MPs, most noticeably by assisting their folding from the denatured state obtained after solubilizing MP inclusion bodies in either SDS or urea. They facilitate the handling in aqueous solution of fragile MPs for the purpose of proteomics, structural and functional studies, and therapeutics. Because APols can be chemically labeled or functionalized, and they form very stable complexes with MPs, they can also be used to functionalize those indirectly, which opens onto many novel applications. Following a brief recall of the properties of APols and MP/APol complexes, an update is provided of recent progress in these various fields.

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Unraveling Hidden Regulatory Sites in Structurally Homologous Metalloproteases

Cited by 53 publications

References 66 publications

Ambidextrous binding of cell and membrane bilayers by soluble matrix metalloproteinase-12

Ambidextrous binding of cell and membrane bilayers by soluble matrix metalloproteinase-12

Discovery of a highly selective chemical inhibitor of matrix metalloproteinase-9 (MMP-9) that allosterically inhibits zymogen activation

Amphipols for Each Season

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