In biology and biochemistry, protease inhibitors, or antiproteases, [1] are molecules that inhibit the function of proteases (enzymes that aid the breakdown of proteins). Many naturally occurring protease inhibitors are proteins. [2]
In medicine, protease inhibitor is often used interchangeably with alpha 1-antitrypsin (A1AT, which is abbreviated PI for this reason). [3] A1AT is indeed the protease inhibitor most often involved in disease, namely in alpha-1 antitrypsin deficiency.
Protease inhibitors may be classified either by the type of protease they inhibit, or by their mechanism of action. In 2004 Rawlings and colleagues introduced a classification of protease inhibitors based on similarities detectable at the level of amino acid sequence. [4] This classification initially identified 48 families of inhibitors that could be grouped into 26 related superfamily (or clans) by their structure. According to the MEROPS database there are now 81 families of inhibitors. These families are named with an I followed by a number, for example, I14 contains hirudin-like inhibitors.
Classes of proteases are:
Classes of inhibitor mechanisms of action are:
This is a family of protease suicide inhibitors called the serpins. It contains inhibitors of multiple cysteine and serine protease families. Their mechanism of action relies on undergoing a large conformational change which inactivates their target's catalytic triad.
Peptidase inhibitor I9 | |||||||||
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![]() subtilisin bpn' prosegment (77 residues) complexed with a mutant subtilisin bpn' (266 residues). crystal ph 4.6. crystallization temperature 20 c diffraction temperature-160 c | |||||||||
Identifiers | |||||||||
Symbol | Inhibitor_I9 | ||||||||
Pfam | PF05922 | ||||||||
InterPro | IPR010259 | ||||||||
MEROPS | I9 | ||||||||
SCOP2 | 1gns / SCOPe / SUPFAM | ||||||||
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Proteinase propeptide inhibitors (sometimes referred to as activation peptides) are responsible for the modulation of folding and activity of the peptidase pro-enzyme or zymogen. The pro-segment docks into the enzyme, shielding the substrate binding site, thereby promoting inhibition of the enzyme. Several such propeptides share a similar topology, despite often low sequence identities. [5] [6] The propeptide region has an open-sandwich antiparallel-alpha/antiparallel-beta fold, with two alpha-helices and four beta-strands with a (beta/alpha/beta)x2 topology. The peptidase inhibitor I9 family contains the propeptide domain at the N-terminus of peptidases belonging to MEROPS family S8A, subtilisins. The propeptide is removed by proteolytic cleavage; removal activating the enzyme.
Serine endopeptidase inhibitors | |||||||||
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![]() solution structure of marinostatin, a protease inhibitor, containing two ester linkages | |||||||||
Identifiers | |||||||||
Symbol | Inhibitor_I10 | ||||||||
Pfam | PF12559 | ||||||||
InterPro | IPR022217 | ||||||||
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This family includes both microviridins and marinostatins. It seems likely that in both cases it is the C-terminus which becomes the active inhibitor after post-translational modifications of the full length, pre-peptide. It is the ester linkages within the key, 12-residue region that circularise the molecule giving it its inhibitory conformation.
PinA peptidase inhibitor | |||||||||
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Identifiers | |||||||||
Symbol | Inhibitor_I24 | ||||||||
Pfam | PF10465 | ||||||||
InterPro | IPR019506 | ||||||||
MEROPS | I24 | ||||||||
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This family includes PinA, which inhibits the endopeptidase La. It binds to the La homotetramer but does not interfere with the ATP binding site or the active site of La.
Cathepsin propeptide inhibitor domain (I29) | |||||||||
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![]() crystal structure of a cysteine protease proform | |||||||||
Identifiers | |||||||||
Symbol | Inhibitor_I29 | ||||||||
Pfam | PF08246 | ||||||||
InterPro | IPR013201 | ||||||||
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The inhibitor I29 domain, which belongs to MEROPS peptidase inhibitor family I29, is found at the N-terminus of a variety of peptidase precursors that belong to MEROPS peptidase subfamily C1A; these include cathepsin L, papain, and procaricain. [7] It forms an alpha-helical domain that runs through the substrate-binding site, preventing access. Removal of this region by proteolytic cleavage results in activation of the enzyme. This domain is also found, in one or more copies, in a variety of cysteine peptidase inhibitors such as salarin. [8]
Saccharopepsin inhibitor I34 | |||||||||
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![]() the structure of proteinase a complexed with an ia3 mutant inhibitor | |||||||||
Identifiers | |||||||||
Symbol | Inhibitor_I34 | ||||||||
Pfam | PF10466 | ||||||||
InterPro | IPR019507 | ||||||||
MEROPS | I34 | ||||||||
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The saccharopepsin inhibitor I34 is highly specific for the aspartic peptidase saccharopepsin. In the absence of saccharopepsin it is largely unstructured, [9] but in its presence, the inhibitor undergoes a conformational change forming an almost perfect alpha-helix from Asn2 to Met32 in the active site cleft of the peptidase.
Peptidase inhibitor family I36 | |||||||||
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![]() the 3d structure of the streptomyces metalloproteinase inhibitor, smpi, isolated from streptomyces nigrescens tk-23, nmr, minimized average structure | |||||||||
Identifiers | |||||||||
Symbol | Inhibitor_I36 | ||||||||
Pfam | PF03995 | ||||||||
Pfam clan | CL0333 | ||||||||
InterPro | IPR007141 | ||||||||
MEROPS | I36 | ||||||||
SCOP2 | 1bhu / SCOPe / SUPFAM | ||||||||
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The peptidase inhibitor family I36 domain is only found in a small number of proteins restricted to Streptomyces species. All have four conserved cysteines that probably form two disulphide bonds. One of these proteins from Streptomyces nigrescens, is the well characterised metalloproteinase inhibitor SMPI. [10] [11]
The structure of SMPI has been determined. It has 102 amino acid residues with two disulphide bridges and specifically inhibits metalloproteinases such as thermolysin, which belongs to MEROPS peptidase family M4. SMPI is composed of two beta-sheets, each consisting of four antiparallel beta-strands. The structure can be considered as two Greek key motifs with 2-fold internal symmetry, a Greek key beta-barrel. One unique structural feature found in SMPI is in its extension between the first and second strands of the second Greek key motif which is known to be involved in the inhibitory activity of SMPI. In the absence of sequence similarity, the SMPI structure shows clear similarity to both domains of the eye lens crystallins, both domains of the calcium sensor protein-S, as well as the single-domain yeast killer toxin. The yeast killer toxin structure was thought to be a precursor of the two-domain beta gamma-crystallin proteins, because of its structural similarity to each domain of the beta gamma-crystallins. SMPI thus provides another example of a single-domain protein structure that corresponds to the ancestral fold from which the two-domain proteins in the beta gamma-crystallin superfamily are believed to have evolved. [12]
Chagasin family peptidase inhibitor I42 | |||||||||
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![]() solution structure of the trypanosoma cruzi cysteine protease inhibitor chagasin | |||||||||
Identifiers | |||||||||
Symbol | Inhibitor_I42 | ||||||||
Pfam | PF09394 | ||||||||
InterPro | IPR018990 | ||||||||
MEROPS | I42 | ||||||||
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Inhibitor family I42 includes chagasin, a reversible inhibitor of papain-like cysteine proteases. [13] Chagasin has a beta-barrel structure, which is a unique variant of the immunoglobulin fold with homology to human CD8alpha. [14] [15]
Peptidase inhibitor clitocypin | |||||||||
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Identifiers | |||||||||
Symbol | Inhibitor_I48 | ||||||||
Pfam | PF10467 | ||||||||
InterPro | IPR019508 | ||||||||
MEROPS | I48 | ||||||||
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Inhibitor family I48 includes clitocypin, which binds and inhibits cysteine proteinases. It has no similarity to any other known cysteine proteinase inhibitors but bears some similarity to a lectin-like family of proteins from mushrooms. [16]
Thrombin inhibitor Madanin | |||||||||
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Identifiers | |||||||||
Symbol | Inhibitor_I53 | ||||||||
Pfam | PF11714 | ||||||||
InterPro | IPR021716 | ||||||||
MEROPS | I53 | ||||||||
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Members of this family are the peptidase inhibitor madanin proteins. These proteins were isolated from tick saliva. [17]
Bromelain inhibitor VI | |||||||||
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![]() nmr structure of bromelain inhibitor vi from pineapple stem | |||||||||
Identifiers | |||||||||
Symbol | Inhibitor_I67 | ||||||||
Pfam | PF11405 | ||||||||
InterPro | IPR022713 | ||||||||
MEROPS | I67 | ||||||||
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Bromelain inhibitor VI, in the Inhibitor I67 family, is a double-chain inhibitor consisting of an 11-residue and a 41-residue chain.
Carboxypeptidase inhibitor I68 | |||||||||
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![]() crystal structure of the tick carboxypeptidase inhibitor in complex with human carboxypeptidase b | |||||||||
Identifiers | |||||||||
Symbol | Inhibitor_I68 | ||||||||
Pfam | PF10468 | ||||||||
InterPro | IPR019509 | ||||||||
MEROPS | I68 | ||||||||
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The Carboxypeptidase inhibitor I68 family represents a family of tick carboxypetidase inhibitors.
Peptidase inhibitor I78 family | |||||||||
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Identifiers | |||||||||
Symbol | Inhibitor_I78 | ||||||||
Pfam | PF11720 | ||||||||
Pfam clan | CL0367 | ||||||||
InterPro | IPR021719 | ||||||||
MEROPS | I78 | ||||||||
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The peptidase inhibitor I78 family includes Aspergillus elastase inhibitor.
A metalloproteinase, or metalloprotease, is any protease enzyme whose catalytic mechanism involves a metal. An example is ADAM12 which plays a significant role in the fusion of muscle cells during embryo development, in a process known as myogenesis.
The cystatins are a family of cysteine protease inhibitors which share a sequence homology and a common tertiary structure of an alpha helix lying on top of an anti-parallel beta sheet. The family is subdivided as described below.
ADAMs are a family of single-pass transmembrane and secreted metalloendopeptidases. All ADAMs are characterized by a particular domain organization featuring a pro-domain, a metalloprotease, a disintegrin, a cysteine-rich, an epidermal-growth factor like and a transmembrane domain, as well as a C-terminal cytoplasmic tail. Nonetheless, not all human ADAMs have a functional protease domain, which indicates that their biological function mainly depends on protein–protein interactions. Those ADAMs which are active proteases are classified as sheddases because they cut off or shed extracellular portions of transmembrane proteins. For example, ADAM10 can cut off part of the HER2 receptor, thereby activating it. ADAM genes are found in animals, choanoflagellates, fungi and some groups of green algae. Most green algae and all land plants likely lost ADAM proteins.
Aspartic proteases are a catalytic type of protease enzymes that use an activated water molecule bound to one or more aspartate residues for catalysis of their peptide substrates. In general, they have two highly conserved aspartates in the active site and are optimally active at acidic pH. Nearly all known aspartyl proteases are inhibited by pepstatin.
Scorpion toxins are proteins found in the venom of scorpions. Their toxic effect may be mammal- or insect-specific and acts by binding with varying degrees of specificity to members of the Voltage-gated ion channel superfamily; specifically, voltage-gated sodium channels, voltage-gated potassium channels, and Transient Receptor Potential (TRP) channels. The result of this action is to activate or inhibit the action of these channels in the nervous and cardiac organ systems. For instance, α-scorpion toxins MeuNaTxα-12 and MeuNaTxα-13 from Mesobuthus eupeus are neurotoxins that target voltage-gated Na+ channels (Navs), inhibiting fast inactivation. In vivo assays of MeuNaTxα-12 and MeuNaTxα-13 effects on mammalian and insect Navs show differential potency. These recombinants exhibit their preferential affinity for mammalian and insect Na+ channels at the α-like toxins' active site, site 3, in order to inactivate the cell membrane depolarization faster[6]. The varying sensitivity of different Navs to MeuNaTxα-12 and MeuNaTxα-13 may be dependent on the substitution of a conserved Valine residue for a Phenylalanine residue at position 1630 of the LD4:S3-S4 subunit or due to various changes in residues in the LD4:S5-S6 subunit of the Navs. Ultimately, these actions can serve the purpose of warding off predators by causing pain or to subdue predators.
Kunitz soybean trypsin inhibitor is a type of protein contained in legume seeds which functions as a protease inhibitor. Kunitz-type Soybean Trypsin Inhibitors are usually specific for either trypsin or chymotrypsin. They are thought to protect seeds against consumption by animal predators.
Kunitz domains are the active domains of proteins that inhibit the function of protein degrading enzymes or, more specifically, domains of Kunitz-type are protease inhibitors. They are relatively small with a length of about 50 to 60 amino acids and a molecular weight of 6 kDa. Examples of Kunitz-type protease inhibitors are aprotinin, Alzheimer's amyloid precursor protein (APP), and tissue factor pathway inhibitor (TFPI). Kunitz STI protease inhibitor, the trypsin inhibitor initially studied by Moses Kunitz, was extracted from soybeans.
In molecular biology, the CHAP domain is a region between 110 and 140 amino acids that is found in proteins from bacteria, bacteriophages, archaea and eukaryotes of the family Trypanosomidae. The domain is named after the acronym cysteine, histidine-dependent amidohydrolases/peptidases. Many of these proteins are uncharacterised, but it has been proposed that they may function mainly in peptidoglycan hydrolysis. The CHAP domain is found in a wide range of protein architectures; it is commonly associated with bacterial type SH3 domains and with several families of amidase domains. It has been suggested that CHAP domain containing proteins utilise a catalytic cysteine residue in a nucleophilic-attack mechanism.
In molecular biology the protein SSI is a Subtilisin inhibitor-like which stands for Streptomyces subtilisin inhibitor. This is a protease inhibitor. These are often synthesised as part of a larger precursor protein, either as a prepropeptide. The function of this protein domain is to prevent access of the substrate to the active site. It is found only in bacteria.
In molecular biology, the Bowman–Birk protease inhibitor family of proteins consists of eukaryotic proteinase inhibitors, belonging to MEROPS inhibitor family I12, clan IF. They mainly inhibit serine peptidases of the S1 family, but also inhibit S3 peptidases.
The Kazal domain is an evolutionary conserved protein domain usually indicative of serine protease inhibitors. However, kazal-like domains are also seen in the extracellular part of agrins, which are not known to be protease inhibitors.
The CAP superfamily is a large superfamily of secreted proteins that are produced by a wide range of organisms, including prokaryotes and non-vertebrate eukaryotes.
In molecular biology, the carboxypeptidase A inhibitor family is a family of proteins which is represented by the well-characterised metallocarboxypeptidase A inhibitor (MCPI) from potatoes, which belongs to the MEROPS inhibitor family I37, clan IE. It inhibits metallopeptidases belonging to MEROPS peptidase family M14, carboxypeptidase A. In Russet Burbank potatoes, it is a mixture of approximately equal amounts of two polypeptide chains containing 38 or 39 amino acid residues. The chains differ in their amino terminal sequence only and are resistant to fragmentation by proteases. The structure of the complex between bovine carboxypeptidase A and the 39-amino-acid carboxypeptidase A inhibitor from potatoes has been determined at 2.5-Angstrom resolution.
In molecular biology, the trappin protein transglutaminase binding domain or cementoin is a protein domain found at the N-terminus of Whey Acidic Protein (WAP) domain-containing protease inhibitors such as trappin-2. This N-terminal domain enables it to become cross-linked to extracellular matrix proteins by transglutaminase. This domain contains several repeated motifs with the consensus sequence Gly-Gln-Asp-Pro-Val-Lys, and these together can anchor the whole molecule to extracellular matrix proteins, such as laminin, fibronectin, beta-crystallin, collagen IV, fibrinogen, and elastin, by transglutaminase-catalysed cross-links. The whole domain is rich in glutamine and lysine, thus allowing transglutaminase(s) to catalyse the formation of an intermolecular epsilon-(gamma-glutamyl)lysine isopeptide bond.
In molecular biology, the dipeptidyl-peptidase IV family is a family of serine peptidases which belong to MEROPS peptidase family S9, subfamily S9B. The protein fold of the peptidase domain for members of this family resembles that of serine carboxypeptidase D, the type example of clan SC. The type example of this family is Dipeptidyl peptidase-4.
In molecular biology, ecotin is a protease inhibitor which belongs to MEROPS inhibitor family I11, clan IN. Ecotins are dimeric periplasmic proteins from Escherichia coli and related Gram-negative bacteria that have been shown to be potent inhibitors of many trypsin-fold serine proteases of widely varying substrate specificity, which belong to MEROPS peptidase family S1. Phylogenetic analysis suggested that ecotin has an exogenous target, possibly neutrophil elastase. Ecotin from E. coli, Yersinia pestis, and Pseudomonas aeruginosa, all species that encounter the mammalian immune system, inhibit neutrophil elastase strongly while ecotin from the plant pathogen Pantoea citrea inhibits neutrophil elastase 1000-fold less potently. Ecotins all potently inhibit pancreatic digestive peptidases trypsin and chymotrypsin, while showing more variable inhibition of the blood peptidases Factor Xa, thrombin, and urokinase-type plasminogen activator.
In molecular biology, haemadin is an anticoagulant peptide synthesised by the Indian leech, Haemadipsa sylvestris. It adopts a secondary structure consisting of five short beta-strands (beta1-beta5), which are arranged in two antiparallel distorted sheets formed by strands beta1-beta4-beta5 and beta2-beta3 facing each other. This beta-sandwich is stabilised by six enclosed cysteines arranged in a [1-2, 3-5, 4-6] disulfide pairing resulting in a disulfide-rich hydrophobic core that is largely inaccessible to bulk solvent. The close proximity of disulfide bonds [3-5] and [4-6] organises haemadin into four distinct loops. The N-terminal segment of this domain binds to the active site of thrombin, inhibiting it.
In molecular biology, the cyanobacterial clock proteins are the main circadian regulator in cyanobacteria. The cyanobacterial clock proteins comprise three proteins: KaiA, KaiB and KaiC. The kaiABC complex may act as a promoter-nonspecific transcription regulator that represses transcription, possibly by acting on the state of chromosome compaction. This complex is expressed from a KaiABC operon.
The 3C-like protease (3CLpro) or main protease (Mpro), formally known as C30 endopeptidase or 3-chymotrypsin-like protease, is the main protease found in coronaviruses. It cleaves the coronavirus polyprotein at eleven conserved sites. It is a cysteine protease and a member of the PA clan of proteases. It has a cysteine-histidine catalytic dyad at its active site and cleaves a Gln–(Ser/Ala/Gly) peptide bond.
Pacifastin is a family of serine proteinase inhibitors found in arthropods. Pacifastin inhibits the serine peptidases trypsin and chymotrypsin.