Research contributes to the design of more effective antibiotics and anticancer compounds
Antibiotic resistance is a very pressing public health issue. Drug resistant bacteria are on the rise, and the number of antibiotics available to fight them are not enough. Infections by drug resistant bacteria is especially a serious problem for people with compromised immune systems, such as cancer and AIDS patients. There is also a tremendous financial burden to patients due to the need for more expensive antibiotics that often have more serious side effects. Scientists and clinicians are thus interested in finding new antibiotics, new targets, and new modes of actions to curtail emerging drug resistant bacteria.
In the cell, an enzyme called ClpP protease is responsible for removing damaged and misfolded proteins by degrading them into smaller fragments. This function is essential in maintaining protein homeostasis, whereby proteins are continually produced and removed in the act of cellular housekeeping, and this in turn sustains the life of the cell. However, this enzyme is also essential in many pathogenic bacteria because its function is linked to their ability to spread infection. Hence, the ClpP protease is one of the new and interesting targets for antibiotic drug discovery.
ClpP activity is normally regulated by chaperone proteins that act as “molecular filters,” selecting only the proper substrate proteins to be removed from the cell. However, certain small molecules have been found to specifically bind to the surface pockets of ClpP and activate its function, even in the absence of regulatory proteins. Consequently, when bound with these so-called small molecule activators, the proteolytic machinery of ClpP has no breaks, and it degrades cellular proteins indiscriminately and uncontrollably. As a result of ClpP dysregulation, bacterial cell death ensues. This forms the basis for the antibiotic potential of small molecule activators.
In addition, hyperactive cancer cells produce an excessive amount of reactive oxygen species which cause increased protein damage. Therefore, in many human tumors, ClpP is overexpressed in the mitochondria as a mechanism to cope with the increased amount of defective proteins. In other words, ClpP overexpression is necessary to sustain the hyperactive cancer cell. It has already been found that small molecule activators of ClpP can cause cancer cell death, but the molecular processes involved are still being uncovered.
In this context, researchers from the University of Toronto and collaborators  studied two classes of small molecule activators called acyldepsipeptides (ADEPs) and Activators of Compartmentalized Proteases (ACPs).
Using a combination of X-ray crystallography, NMR, and SAXS (at the SAXS1 beamline of the Brazilian Synchrotron Light Laboratory), the researchers investigated the mechanism by which these molecules activate the ClpP protease by identifying the structural effects caused by activator binding. The new structures of ClpP with bound activators led to the discovery of a common activation mechanism used by different classes of small molecule activators.
The group found that the minimum requirement for ClpP activation is the reorganization of the electrostatic interactions near the axial pores of the protease. The binding of the small molecule activators causes this reorganization which, in turn, leads to a cascade of structural changes, including axial pore opening and structure rigidification, which are important features of a fully activated ClpP.
According to the researchers, a spectrum of activity exists for ClpP, depending on how many structural features characteristic of active species are induced by the binding of small molecule activators. These discoveries lead to a deeper understanding of the ClpP activation process and contribute to the design of better and more effective antibiotics and anticancer compounds.
Source:  Mark F. Mabanglo, Elisa Leung, Siavash Vahidi, Thiago V. Seraphim, Bryan T. Eger, Steve Bryson, Vaibhav Bhandari, Jin Lin Zhou, Yu-Qian Mao, Kamran Rizzolo, Marim M. Barghash, Jordan D. Goodreid, Sadhna Phanse, Mohan Babu, Leandro R.S. Barbosa, Carlos H. I. Ramos, Robert A. Batey, Lewis E. Kay, Emil F. Pai, Walid A. Houry, ClpP protease activation results from the reorganization of the electrostatic interaction networks at the entrance pores. Commun. Biol. 2, 410 (2019) doi:10.1038/s42003-019-0656-3