Probing the conformational transition of pathogens adenyl cyclases

As the molecular interactions play a key role in biological processes, they are preferential targets for drug discovery. Nevertheless, the description of such interactions presents a major challenge for computational physics. It will be shown here that this challenge can be taken up using computational methods for conformational landscape exploration, along with more classical experimental and modeling tools. The adenyl cyclases EF and CyaA are essential toxins for the pathogens Bacillus anthracis (anthrax) and Bordetella pertussis (whooping cough), and are activated by binding to calmodulin. CaM binding to EF induces a major transition which activates the protein as toxins. The structures of closed EF (free protein) and open EF (bound to CaM) were determined by X-ray crystallography [1], whereas only the structure CyaA bound to CaM is known [2]. Analysis of the hydrodynamic parameters of CyaA [3] in the absence of CaM revealed strong structure reorganization. Several original approaches were employed to dissect the structural determinants of the interactions between adenyl cyclases and CaM. First, energetics of the complexes with CaM were analyzed by determining Energetic Dependency Maps (EDM) [4], and the hierarchy of relative stabilities given by the EDM put in evidence the importance of the region of switches SA, SB and SC in the molecular interaction mechanism. Second, a path describing the conformational transition between the closed and open forms of the protein EF was calculated [5, 6] using the knowledge of the molecular structures at the two ends of the transition. A putative allosteric binding site, located at the interface between switches SA, SB and SC, was then identified on the path, and candidate EF inhibitors were proposed using virtual screening. A series of thiophen ureidoacids was then experimentally proved to inhibit EF activation and were also shown to inhibit moderately CyaA [7].