This project has two main elements. The major effort began two years ago and involved collaboration with scientists at the NIH Chemical Genomics Center (NCGC) to conduct a high-throughput screen (HTS) of a large chemical library to search for compounds that activate ClpP peptidase and protease activity in a manner similar to the ADEP antibiotics. This project was partially funded through an R03 award (1 R03 MH095569) granted to me in 2012. The interactions between ADEP and ClpP, as shown by X-ray crystallography, suggest that there should be a high likelihood of finding organic molecules that display a rigid structure that mimics the aromatic/aliphatic part of ADEP, dock to ClpP, and exert allosteric effects on its activity. The primary contacts between ADEP and ClpP involve hydrophobic interactions between an aromatic ring in ADEP and a deep pocket on the apical surface of ClpP. In addition, there are hydrophobic interactions between an aliphatic chain in ADEP and a hydrophobic groove that extends from the hydrophobic pocket toward the axial channel of ClpP. Other minor interactions include hydrogen binding involving backbone atoms from a short peptide segment of ADEP. The depsipeptide portion of ADEP has very little interaction with ClpP and serves primarily to restrict the conformational flexibility of the aliphatic regions in ADEP, which are fixed in a configuration that locks into the docking site. The solution structure of ADEP alone confirms that there is little induced change in its upon binding to ClpP. After a large scale screening of over 300,000 compounds, about 18 compounds were identified as potential inhibitors of ClpP and about 30 were identified as potential activators. The compounds are now being tested in more detail for their effects on various activities of ClpP. Compounds that that are identified as validated activators of inhibitors will be provided in larger quantities for further studies and for structural studies to identify the sites and mode of binding. They will be assayed further in my laboratory to obtain a more complete profile of binding affinity, activating effect on both peptide and protein substrates, and comparative specificity for human, E. coli, and B. subtilis ClpPs. Compounds will then be tested for antimicrobial activity against laboratory strains of E. coli and B. subtilis. Compounds will also be tested for their growth inhibitory activity against several human cancer cell lines. Once promising lead compounds have been identified and screened by the various secondary assays mentioned, the synthetic chemistry team at NCGC will begin designing synthetic strategies for making the compounds and variations of the compounds to develop new versions that are optimized for binding to ClpP and for effectiveness against cultures of bacteria. To complement the efforts to identify new compounds that mimic ADEPs in their binding to ClpP, we conducted a genetic screen to obtain mutants of ClpP that have altered binding properties and possibly altered allosteric responses to binding of ADEP. ADEPs bind to the docking site on the apical surface of ClpP used by ClpX and ClpA/C in forming the biologically functional ClpXP and ClpAP complexes. We developed a sensitive selection procedure that identified mutants of ClpP that were resistant to ADEP but retained enzymatic activity with ClpX. The selection was based on the ability of ClpXP to degrade proteins with an 11-amino acid degradation tag (called an SsrA tag) at the C-terminus. From a group of multiply mutated ClpPs we have isolated six forms of ClpP bearing single mutations. Cells expressing the mutants retain activity in degrading the SsrA-tagged protein and are resistant to ADEP to varying degrees. We have purified the mutant proteins are in the process of studying their biochemical and enzymatic activities in vitro. The goal of this work is to identify the critical residues in ClpP that are involved in both binding of ADEPs and ClpX and in the allosteric response that communicates to the axial channel and causes the channel to be expended and allow indiscriminate protein entry. Mutated forms of ClpP that respond differently to ADEP and ClpX could show different binding affinity or binding rates or could be affected in residues that make new interactions that stabilize the activated structure of ClpP. In a related effort, we have initiated an effort to synthesize beta-lactone inhibitors of ClpP. Initially we are making two inhibitors that have been described in the literature, and plans are to make modifications to the procedure to introduce other substituents that should contribute additional binding affinity to ClpP. These inhibitors will be reacted with purified ClpP to study the effects on the quaternary structure and to obtain crystal structure data to elucidate how they are bound in the ClpP active site.
| Zhang, Yang; Maurizi, Michael R (2016) Mitochondrial ClpP activity is required for cisplatin resistance in human cells. Biochim Biophys Acta 1862:252-64 |
