Discovery of Novel Peptidomimetic Boronate ClpP Inhibitors with Noncanonical Enzyme Mechanism as Potent Virulence Blockers in Vitro and in Vivo

Abstract

Caseinolytic protease P (ClpP) is considered as a promising target for the treatment of Staphylococcus aureus infections. In an unbiased screen of 2632 molecules, a peptidomimetic boronate, MLN9708, was found to be a potent suppressor of SaClpP function. A time-saving and cost-efficient strategy integrating in silico position scanning, multistep miniaturized synthesis, and bioactivity testing was deployed for optimization of this hit compound and led to fast exploration of structure−activity relationships. Five of 150 compounds from the miniaturized synthesis exhibited improved inhibitory activity. Compound 43Hf was the most active inhibitor and showed reversible covalent binding to SaClpP while did not destabilize the tetradecameric structure of SaClpP. The crystal structure of 43Hf-SaClpP complex provided mechanistic insight into the covalent binding mode of peptidomimetic boronate and SaClpP. Furthermore, 43Hf could bind endogenous ClpP in S. aureus cells and exhibited significant efficacy in attenuating S. aureus virulence in vitro and in vivo.

Armeniaspirols inhibit the AAA+ proteases ClpXP and ClpYQ leading to cell division arrest in Gram-positive bacteria

“…ClpXP has been identified as a promising target for drug development due to its significant role in regulating virulence in diverse pathogens [19][20][21][22]133,134 . Pioneering work has uncovered synthetic β-lactone-, phenyl ester-, and boronate-based inhibitors of ClpXP [135][136][137] . While promising, significant challenges including resistance, stability, and potential reduction of susceptibility to other antibiotics exist for these ClpP inhibitors 136,[138][139][140] .…”

Recent developments in the medicinal chemistry of single boron atom-containing compounds

“…Ju et al . 100 screened 2632 molecules and selected a peptidomimetic boronate, MLN9708 ( 49 ) with an IC 50 value of 5.7 μmol/L against Sa ClpP for further optimization. Based on the idea that boron binds to residue Ser98 in the Sa ClpP active site, they constructed a virtual library of boron-based compounds and modeled the binding to the active site of Sa ClpP.…”

Function, molecular mechanisms, and therapeutic potential of bacterial HtrA proteins: An evolving view

“…Bacterial proteases are promising targets for the development of new antibiotics. Synthetic inhibitors of ClpXP proteases are potential agents active against Mycobacterium tuberculosis and Staphylococcus aureus [71] , [72] . In a recent review, Xue et al .…”