Chemical Modulation of Human Mitochondrial ClpP: Potential Application in Cancer Therapeutics

Abstract

The human ClpP proteolytic complex (HsClpP) is a serine protease located in the mitochondrial matrix and participates in the maintenance of the mitochondrial proteome among other cellular functions. HsClpP typically forms a multimeric complex with the AAA+ protein unfoldase HsClpX. Notably, compared to that of normal, healthy cells, the expression of HsClpP in many types of solid and nonsolid cancers is found to be upregulated. While the exact role of HsClpP in tumorigenesis is not clear, certain types of cancers are highly dependent on the protease for cell proliferation and metastasis. In light of these observations, recent research has focused on the discovery and characterization of small organic molecules that can target and modulate HsClpP activity. These include compounds that inhibit HsClpP's proteolytic activity via covalent modification of its catalytic Ser residue as well as those that activate and dysregulate HsClpP by displacing HsClpX to negate its regulatory role. Importantly, several of these compounds have been shown to induce HsClpP-dependent apoptotic cell death in a variety of cancerous cells. This review provides an overview of these research efforts and highlights the various types of small molecule modulators of HsClpP activity with respect to their potential use as cancer therapeutics.

Imipridone Anticancer Compounds Ectopically Activate the ClpP Protease and Represent a New Scaffold for Antibiotic Development

“…X-ray structures show that ONC201, ADEPs, and D9 all occupy the same binding site in human CLPP (Stahl et al 2018;Wong et al 2018;Ishizawa et al 2019;Wong and Houry 2019). Although comparison of these human CLPP structures with several bacterial ClpP structures reveals that the binding pocket is highly conserved ( Figure S5), divergent features of the pocket might nevertheless allow species-specific activators to be developed (Bhandari et al 2018;Wong and Houry 2019). Indeed, D9 is only active against human CLPP (Stahl et al 2018) and some ADEP analogs exert species-specific effects (Goodreid et al 2016;Wong et al 2018).…”

“…Drug-induced activation of either human CLPP or bacterial ClpP is a promising strategy for both anticancer (Bhandari et al 2018;Wong et al 2018;Wong and Houry 2019) and anti-infective drug discovery (Culp and Wright 2017;Bhandari et al 2018). However, the potential cross-activation of human CLPP and bacterial ClpP by the current generation of imipridones raises the issue of unintended collateral effects.…”

“…A number of compounds have been identified as ClpP activators, including the ADEPs and a variety of (semi)-synthetic analogs (Brötz-Oesterhelt et al 2005;Carney et al 2014b;Goodreid et al 2016;Wong et al 2018;Griffith et al 2019), ADEP-based fragments (Carney et al 2014a), the imipridones and the related TR series compounds (Allen et al 2013;Graves et al 2019;Ishizawa et al 2019;Wong and Houry 2019), the natural product sclerotiamide (Lavey et al 2016), and the synthetic compounds D9 (Stahl et al 2018) and ACP1 (Leung et al 2011). X-ray structures show that ONC201, ADEPs, and D9 all occupy the same binding site in human CLPP (Stahl et al 2018;Wong et al 2018;Ishizawa et al 2019;Wong and Houry 2019). Although comparison of these human CLPP structures with several bacterial ClpP structures reveals that the binding pocket is highly conserved ( Figure S5), divergent features of the pocket might nevertheless allow species-specific activators to be developed (Bhandari et al 2018;Wong and Houry 2019).…”

“…ADEPs inhibit the growth of Gram-positive pathogens by causing massive unregulated intracellular proteolysis (Brötz-Oesterhelt et al 2005), and when used in combination with other antibiotics can efficiently eradicate antibiotic-tolerant persister cells (Conlon et al 2013). Even though ADEPs and various synthetic analogs demonstrate the potential of ClpP as a drug target (Bhandari et al 2018;Wong and Houry 2019), the low solubility, chemical instability, and poor pharmacodynamics of ADEPs have hampered therapeutic development (Brötz-Oesterhelt et al 2005;Moreno-Cinos et al 2019).…”

Polymerase delta-interacting protein 38 (PDIP38) modulates the stability and activity of the mitochondrial AAA+ protease CLPXP

“…Consistently, mammalian CLPXP is reported to play a critical role in a variety of important functions, including mitoribosome assembly 12 and haem regulation 11 , 13 , 14 . Likewise, compounds that dysregulated mitochondrial CLPP 15 exhibit therapeutic potential against specific cancer cells 16 – 18 . Despite the emerging importance of this protease in human health and disease, only a handful of CLPXP substrates have been verified.…”