One cannot rule them all: Are bacterial toxins-antitoxins druggable?

Chan, Wai Ting; Balsa, Dolors; Espinosa, Manuel

New technologies aimed at characterization of the contact surface between two interacting proteins, in conjunction to methodologies based on structure-based design, have facilitated the detection of small molecules that act as i-PPIs. The identification of compounds that may act as i-PPIs seems to be attainable by computational drug design (Bienstock 2012 ). There are a number of strategies that have been employed to check for hotspot regions in the protein-protein interfaces, such as protein crystallography to elucidate the 3D protein structure, molecular docking, virtual screening and approaches to design novel drug libraries (reviewed in depth by Bienstock 2012 and Huang 2014) , although there is a strong need to have curated databases to help in the discovery of PPI-modulators (see, for instance: http://www.vls3d.com/). Development of novel databases to assist the finding and design of novel i-PPIs should prove to be useful for these purposes (Labbé et al., 2013) . A number of TA structures have been solved, which would lead to a more thorough approach to find small molecules that are able to disrupt the T:A interactions, for which the design should be customized since hydrophobic residues seem to dominate the interfaces between the toxin and its cognate antitoxin (Loris et al., 1999; Hargreaves et al., 2002; Kamada, Hanaoka and Burley 2003; Takagi et al., 2005; Kamphuis et al., 2007; Oberer et al., 2007; Kumar et al., 2008; Brown et al., 2009; Francuski and Saenger 2009; Miallau et al., 2009; Arbing et al., 2010; Dienemann et al., 2011; Bøggild et al., 2012; Heaton et al., 2012; Kwon et al., 2012; Feng et al., 2013; Schureck et al., 2014) . Structural Figure 4 . Combination of combinatorial chemistry with high throughput has contributed to the development of large screening libraries of compounds. However, the largest imaginable collection of compounds falls short of potential chemical diversity space. As molecular size decreases, the number of possible molecules decreases exponentially. Thus, at least from a theoretical point of view, it would result easier to screen large collections of very small molecules ('fragments') and, later on proceed to expand, merge or link them. Fragment screening is an excellent method for the identification and validation of lead compounds that can later on be tested for development of therapeutic agents. Fragments are small (MW <300 Da) and can provide the sampling of chemical space more effectively than other screening methods. Highly ligand efficient hits have been identified for several soluble proteins and for i-PPIs purposes. Determination of the 3D structure of the target proteins in conjunction to compounds with a greater degree of 3D shape is a good method to increase the diversity of libraries. Finally, through different rounds of chemical modifications and/or combination with other molecules, fragments with increased affinity for the target protein can be developed. knowledge on TAs should enable us to get a better understanding on the surface contacts between the two protein pairs so that development of inhibitors is facilitated (Park, Mann and Li 2013) . These approaches could be refined by employment of selected databases dedicated to PPIs that have already known inhibitors, so that small molecules can be taken as examples to construct guidelines to characterize i-PPIs (http://2p2idb.cnrs-mrs.fr).