page_title: Acyldepsipeptide antibiotics
section_title: Mechanism
hierarchical_section_title: Acyldepsipeptide antibiotics / Mechanism
caption_attribution_description: English: 1. ClpP cannot degrade protein chains longer than 5 peptides because they are bigger than its proteolytic channel. 2. ClpP requires an ATPase to unfold big proteins, allowing them to pass through ClpP's channel. 3. When ADEPs bind to ClpP, the ATPase/ClpP complex dissociate. 4. The proteolytic channel of ClpP becomes large enough to degrade the proteins without the help of any ATPase.
context_page_description: Acyldepsipeptide or cyclic acyldepsipeptide is a class of potential antibiotics first isolated from bacteria and act by deregulating the ClpP protease. Natural ADEPs were originally found as products of aerobic fermentation in Streptomyces hawaiiensis, A54556A and B, and in the culture broth of Streptomyces species, enopeptin A and B. ADEPs are of great interest in drug development due to their antibiotic properties and thus are being modified in attempt to achieve greater antimicrobial activity.
  The potential role of ADEPs in combating antibiotic drug resistance is postulated due to their novel mode of action that other antibiotics are not known to use, activation of casein lytic protease which is an important bacterial protease. Most antibiotics work through inhibitory processes to establish cell death, while ADEPs actually work through activation of the protease to cause uncontrolled protein degradation, inhibition of cell division, and subsequent cell death.
context_section_description: ADEP antibiotics can be used to defeat resistant bacterial infections. They bind to ClpP and allow the protease to degrade proteins without the help of an ATPase. ADEP4/ClpP complexes target primarily newly formed proteins, and FtsZ which allows cell division. ClpP active form is a tetradecamer composed of two heptamers to which 14 ADEPs bind to.
  ADEPs bind in the cavities formed by two ClpP monomers. Their binding site is composed of hydrophobic residues and corresponds to the binding sites of ClpP ATPases. Upon binding, a series of secondary structures shifts occur from the outer region to the center of ClpP. This puts the flexible N-terminal β-loop, into a disordered state. The β-loops normally form a gate above the proteolytic channel and prevent proteins from randomly passing through. They are critical for ClpP interaction with its substrate and ATPases. When ADEP binds, the β-loops shift outward and this is accompanied by the shifts of two α-helices (α1 and α2), four β-strands (β1, β2, β3 and β5) and other loops which lead to the opening of the ClpP pore. In summary, ADEP4 deregulates ClpP function and changes it from a closed state to an open one. At this point its specific proteolytic activity becomes a less controlled process, with the destruction of proteins that are around in the targeted cell.
  The peptidase ClpP is highly conserved throughout organisms and is tightly regulated. Without activation, ClpP in normal conditions can degrade short peptides that freely diffuse into its inner degradation chamber. Clp-family proteins are ATP-dependent proteases which play a crucial role in the cell function by degrading misfolded proteins. ClpP is a monomer on its own but oligomerizes into tetradecamers when bound to ATPases.  It needs an ATPase to identify, unfold, and transfer targeted big proteins into its proteolytic channel. In fact, ClpP on its own can only degrade peptides that are up to six amino acids long.
  ADEP binding induces ClpP proteolytic activation that leads to the proteins degradation in the cell, especially nascent proteins and the Ftsz protein which is an important protein in cell division. This potentially leads to cell death and is the reason why ADEP is a promising technique for drug development.
  For folded proteins, unfolded proteins, and long peptides, ClpP must be activated by a protein in the family of ATPase associated with diverse cellular activities (AAA proteins), such as ClpA, ClpX, or ClpC. These chaperone proteins are responsible for hydrolyzing ATP to ADP, harnessing the energy, and then taking folded proteins and unfolding them. Next, Clp-ATPases slip the unfolded proteins into the degradation chamber within ClpP, allowing for processive degradation of the substrate. This process is tightly regulated with the hydrolysis of ATP to prevent uncontrolled protein or peptide degradation that would be harmful to the cell.
  In contrast, ADEP activates ClpP without the need for ATP hydrolysis, causing degradation of unfolded proteins and peptides within the cell at uncontrolled rates. ADEPs are thought to bind slightly cooperatively on the surface of each ClpP ring in its hydrophobic pockets and have allosteric effects in activation of ClpP. This binding initiates ClpP to undergo a conformational change such that its N-terminal region opens up its axial pore to allow for partial degradation of products, as compared to progressive degradation with ClpA. ADEP activation of ClpP does not allow for folded protein degradation, but even with unfolded protein and peptide degradation, ADEP still causes bacterial cell death.
  Research has shown that ADEP-activated ClpP targets cell division rather than metabolic processes. ADEP appears to initiate ClpP to preferably degrade FtsZ, an important bacterial protein involved in septum formation that is necessary for bacterial cell division. As a result, Gram-positive bacteria treated with ADEPs form long filaments before cell death.
caption: 1. ClpP cannot degrade protein chains longer than 5 peptides because they are bigger than its proteolytic channel. 2. ClpP requires an ATPase to unfold big proteins, allowing them to pass through ClpP's channel. 3. When ADEPs bind to ClpP, the ATPase/ClpP complex dissociate. 4. The proteolytic channel of ClpP becomes large enough to degrade the proteins without the help of any ATPase.
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