Matrix Metalloproteinases Inhibition: Comparison
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Matrix metalloproteinases are enzymes that degrade the extracellular matrix. They have different substrates but similar structural organization. Matrix metalloproteinases are involved in many physiological and pathological processes and there is a need to develop inhibitors for these enzymes in order to modulate the degradation of the extracellular matrix (ECM). There exist two classes of inhibitors: endogenous and synthetics. The development of synthetic inhibitors remains a great challenge due to the low selectivity and specificity, side effects in clinical trials, and instability. 

  • matrix metalloproteinases
  • TIMP
  • synthetic inhibitors

1. Introduction

Matrix metalloproteinases (MMPs) are a protein family within the metzincin superfamily, comprising zinc-dependent endopeptidases with similar structural characteristics but with different substrate preferences. MMPs are produced and secreted from cells as inactive proenzymes depending, herein, on a structural alteration for activation [1,2,3,4,5,6][1][2][3][4][5][6]. In human tissues, there are 23 different types of MMPs expressed and they can be subdivided according to their substrate specificity, sequential similarity, and domain organization [1,2,4,7,8,9,10,11,12,13,14,15,16,17][1][2][4][7][8][9][10][11][12][13][14][15][16][17] (Table 1).
Table 1. Matrix metalloproteinases (MMPs) classes.
Class MMP
Collagenases MMP-1, Collagenase-1, Interstitial or Fibroblast collagenases
MMP-8, Collagenase-2, or Neutrophil collagenases
MMP-13 or Collagenase 3
Gelatinases MMP-2 or Gelatinase A
MMP-9 or Gelatinase B
Stromelysin MMP-3 or Stromelysin-1
MMP-10 or Stromelysin-2
MMP-11
Matrilysin MMP-7
MMP-26, Matrilysin-2, or Endometase
Membrane-type Type I transmembrane protein MMP-14 or MT1-MMP
MMP-15 or MT2-MMP
MMP-16 or MT3-MMP
MMP-24 or MT5-MMP
Glycosylphosphatidylinositol (GPI)-anchored MMP17 or MT4-MMP
MMP-25 or MT6-MMP
Other MMPs MMP-12
MMP-19
MMP-20
MMP-21
MMP-23
MMP-27
MMP-28
The most common structural features shared by MMPs are [1,2,4,5,7,8,10,11,12,13,14,16,18][1][2][4][5][7][8][10][11][12][13][14][16][18] (Figure 1) a pro-domain, a catalytic domain, a hemopexin-like domain, and a transmembrane domain for membrane-type MMPs (MT-MMPs) although some MMPS do not have all the structural features represented in the figure. The pro-domain keeps MMP inactive by a cysteine switch, which interacts with the catalytic zinc making it impossible to connect the substrate. The catalytic domain has two zinc ions, three calcium ions, and three histidine residues, which are highly conserved [1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,19,20][1][2][3][4][5][6][7][8][9][11][12][13][14][15][16][17][18][19][20]. In the terminal zone of the catalytic domain, there is a region that forms the outer wall of the S1’ pocket [1,14,17][1][14][17]. This pocket is the most variable region in MMPs and it is a determining factor for substrate specificity [1,2,6,7,11,17,18][1][2][6][7][11][17][18]. However, there are six pockets (P1, P2, P3, P1’, P2’, and P3’) and the fragments of the substrates or inhibitors are named depending on the interaction with these pockets (R1, R2, R3, R1’ or Ra, R2’, and R3’). The linker is proline-rich, of variable length, allowing inter-domain flexibility and enzyme stability [4,8,12,13][4][8][12][13]. The hemopexin-like domain is necessary for collagen triple helix degradation and is important for substrate specificity [3,4,7,9,19][3][4][7][9][19].
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Figure 1. Schematic representation of the general structure of MMP.
The MMPs can process ECM proteins and glycoproteins, membrane receptors, cytokines, hormones, chemokines, adhesion molecules, and growth factors [1,3,4,6,7,9,10,11,13,14,20,21,22,23,24,25,26][1][3][4][6][7][9][10][11][13][14][20][21][22][23][24][25][26]. However, the presence and the activity of MMPs have been demonstrated to be intracellular [25,26][25][26]. For example, some studies show intracellular localization of MMP-2 in cardiac myocytes and colocalization of MMP-2 with troponin I in cardiac myofilaments [23]. The MMP-2 activity has also been detected in nuclear extracts from the human heart and rat liver [23]. The MMPs are involved in many biologic processes, such as tissue repair and remodulation, cellular differentiation, embryogenesis, angiogenesis, cell mobility, morphogenesis, wound healing, inflammatory response, apoptosis, ovulation, and endometrial proliferation [1,2,4,6,8,10,11,13,16,17,18,20,27][1][2][4][6][8][10][11][13][16][17][18][20][27]. The deregulation of MMPs activity leads to the progression of various pathologies depending on which enzyme is involved [1,6,10,13,14,15,16,17,20,27][1][6][10][13][14][15][16][17][20][27]: cancer and metastasis, inflammatory processes, arthritis, ulcers, periodontal diseases, brain degenerative diseases, liver cirrhosis, fibrotic lung diseases, otosclerosis, atherosclerosis, multiple sclerosis, dilated cardiomyopathy, aortic aneurysm, or varicose veins.
Although therapeutic strategies for specific inhibition of MMPs have been long researched, they are difficult to develop because these enzymes are involved in a myriad of pathways [2,5][2][5]. However, this inhibition can be done at the biomolecular expression and active enzyme terms [2,5,18][2][5][18]. The MMPs inhibitors can be divided into endogenous inhibitors, which can be specific or non-specific, and synthetic inhibitors [1,2,4,7,10,12,13,14,16,20,28,29][1][2][4][7][10][12][13][14][16][20][28][29] (Table 2).
Table 2. MMPs inhibitors classification.
  Specific Inhibitor Tissue Inhibitor of Metalloproteinases (TIMP)
Endogenous inhibitor Non-specifics inhibitors α2-macroglobulin
Tissue factor pathway inhibitor (TFPI)
The membrane-bound β-amyloid precursor protein
C-terminal proteinases enhancer protein
Reversion-inducing cysteine-rich protein with Kasal domain motifs (RECK)
GPI-anchored glycoprotein
Synthetic inhibitor Hydroxamate-based inhibitors
Non-hydroxamate-based inhibitors
Catalytic domain (non-zinc binding) inhibitors
Allosteric and exosite inhibitors
Antibody-based inhibitors

2. Specific Endogenous Inhibitor-Tissue Inhibitors of Metalloproteinases (TIMPs)

Tissue inhibitors of metalloproteinases (TIMPs) are endogenous proteins responsible for the regulation of MMPs activity, but also of families such as the disintegrin metalloproteinases (ADAM and with thrombospondin motifs ADAMTS) and therefore for maintaining the physiological balance between ECM degradation and MMPs activity [1,2,8,9,18,30][1][2][8][9][18][30]. There are four TIMPs (TIMP-1, -2, -3, and -4) (Table 3), with 22–29 KDa and 41%–52% sequential similarity [2,4,12,13,16,20,31][2][4][12][13][16][20][31].
Table 3. Tissue inhibitors of metalloproteinases (TIMPs) classification.
TIMP Expression Inhibition Inhibition Mode
1 Several tissues with transcription inducible by cytokines and hormones Strong interaction with MMP-1, -2, -3, and -9

Weak interaction with MT1-MMP, MT3-MMP, MT5-MMP, and MMP-19		 TIMP-1 forms a complex with pro-MMP-9 by binding to the hemopexin domain
2 Constitutive expression Strong interaction with MMP-2 TIMP-2 has four residues in the N-terminal domain and an adjacent CD-loop region, which allows interaction between TIMP and the active center of MMP-2
3 In response to mitogenic stimulation and during cell cycle progression MMP-1, -2, -3, -9, and -13 The inhibition mode is different from the other TIMPs for its unusual localization, as it is largely sequestered into the extracellular matrix or at the cell surface via heparan sulphate proteoglycans
4 Especially abundant in the heart, but is also expressed in injured tissue MMP-2 and -14 -
TIMPs consist of a N- and C-terminal domain with 125 and 65 amino acids, respectively, each containing six conserved cysteine residues, which form three conserved disulphide bonds [2,4,7,8,9,12,31,32][2][4][7][8][9][12][31][32] (Figure 2a). The N-terminal domain is an independent unit, which can be inhibited by MMPs, in a 1:1 ratio [2,4,8,9,10,12,13,16,20][2][4][8][9][10][12][13][16][20]. This domain has two groups of four residues: Cys-Thr-Cys-Val and Glu-Ser-Val-Cys (Figure 2b), which are connected by disulphide bonds which are important for TIMP activity [7,12][7][12]. This is the main domain responsible for MMP inhibition through its binding to the catalytic site in a substrate-like manner [31]. The several domains allow the TIMP and pro-gelatinases interactions [4].
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Figure 2. (a) TIMP-1-catalytic domain of the MMP-3 complex. (b) TIMP-1-catalytic domain of the MMP-3 complex, where two conserved groups, Cys-Thr-Cys-Val and Glu-Ser-Val-Cys, are represented in yellow.

3. Non-Specific Endogenous Inhibitors

Non-specific endogenous inhibitors have been reported to inhibit MMPs (Table 4), however, the inhibition mechanism details have only been partially discovered [7,12][7][12].
Table 4. Non-specific endogenous inhibitors [4,7,12,13,33,34][4][7][12][13][33][34].
Non-Specific Inhibitor Inhibition
α2-macroglobulin MMP-2 and -9
Tissue factor pathway inhibitor MMP-1 and -2
Membrane-bound β-amyloid precursor protein MMP-2
C-terminal proteinase enhancer protein MMP-2
Reversion-inducing-cysteine-rich protein with Kasal motifs (RECK) MMP-2, -9, and -14
GPI-anchored glycoprotein -
Human α2-macroglobulin is a glycoprotein with four identical subunits that act by entrapping MMP and the complex is cleared by endocytosis [2]. The α2-macroglobulin has been found in blood and tissue fluid [2,31][2][31]. The tissue factor pathway inhibitor (TFPI) is a serine proteinase inhibitor, which targets MMP-1 and -2, but this inhibition mode is still unknown [7,12][7][12]. The C-terminal proteinase enhancer protein and tissue factor pathway inhibitor have sequences with certain similarities to the N-terminal domain of TIMPs [31].

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