BackgroundIn 2017 World Health Organization announced the list of the most dangerous superbugs and among them is Pseudomonas aeruginosa, which is an antibiotic resistant opportunistic human pathogen as well as one of the ‘SKAPE’ pathogens. The central problem is that it affects patients suffering from AIDS, cystic fibrosis, cancer, burn victims etc. P. aeruginosa creates and inhabits surface-associated biofilms. Biofilms increase resistance to antibiotics and host immune responses, because of those current treatments are not effective. It is imperative to find new antibacterial treatment strategies against P. aeruginosa, but detailed molecular properties of the LasR protein are not clearly known to date. In the present study, we tried to analyse the molecular properties of the LasR protein as well as the mode of its interactions with autoinducer (AI) the N-3-oxododecanoyl homoserine lactone (3-0-C12-HSL).ResultsWe performed docking and molecular dynamics (MD) simulations of the LasR protein of P. aeruginosa with the 3-0-C12-HSL ligand. We assessed the conformational changes of the interaction and analysed the molecular details of the binding of the 3-0-C12-HSL with LasR. A new interaction site of the 3-0-C12-HSL with LasR protein was found, which involves interaction with conservative residues from ligand binding domain (LBD), beta turns in the short linker region (SLR) and DNA binding domain (DBD). It will be referenced as the LBD-SLR-DBD bridge interaction or “the bridge”. We have also performed LasR monomer protein docking and found a new form of dimerization.ConclusionsThis study may offer new insights for future experimental studies to detect the interaction of the autoinducer with “the bridge” of LasR protein and a new interaction site for drug design.

Background: Pseudomonas aeruginosa is one of the most dangerous superbugs in the list of

Store-operated calcium entry (SOCE) constitutes a fine-tuning mechanism responsible for the replenishment of intracellular stores. Hippocampal SOCE is regulated by store-operated channels (SOC) organized in tripartite complex TRPC6/ORAI2/STIM2. It is suggested that in neurons, SOCE maintains intracellular homeostatic Ca2+ concentration at resting conditions and is needed to support the structure of dendritic spines. Recent evidence suggests that positive modulators of SOC are prospective drug candidates to treat Alzheimer’s disease (AD) at early stages. Although STIM2 and ORAI2 are definitely involved in the regulation of nSOC amplitude and a play major role in AD pathogenesis, growing evidence suggest that it is not easy to target these proteins pharmacologically. Existing positive modulators of TRPC6 are unsuitable for drug development due to either bad pharmacokinetics or side effects. Thus, we concentrate the review on perspectives to develop specific nSOC modulators based on available 3D structures of TRPC6, ORAI2, and STIM2. We shortly describe the structural features of existing models and the methods used to prepare them. We provide commonly used steps applied for drug design based on 3D structures of target proteins that might be used to develop novel AD preventing therapy.

Background: In 2017, the World Health Organization announced a list of the most dangerous superbugs. Among them is Pseudomonas aeruginosa, an opportunistic human pathogen with high levels of resistance to antibiotics that is listed as one of the ‘ESKAPE’ pathogens, which are the leading cause of nosocomial infections. A major issue is that it mostly affects vulnerable patients such as those suffering from AIDS, cystic fibrosis, cancer and severe burns. P. aeruginosa creates and inhabits surface-associated biofilms which increase resistance to antibiotics and host immune responses and contribute to the ineffectiveness of current antibacterial treatments. It is therefore imperative to find new antibacterial treatment strategies against P. aeruginosa. The LasR protein is a major transcriptional activator of P. aeruginosa and plays a pivotal role in biofilm formation and the activation of many virulence genes, although detailed characteristics of the LasR protein are not currently known. In the present study, we aimed to analyse the molecular properties of the LasR protein as well as its interactions with the signalling molecule N-3-oxododecanoyl homoserine lactone (3OC12-HSL). Methods: We used a combination of molecular docking, molecular dynamics (MD) simulations and machine learning techniques to study the interaction of the LasR protein with the 3OC12-HSL ligand. We assessed conformational changes occurring upon their interaction and analysed the molecular details of their binding. Results: A new possible interaction site for 3OC12-HSL and LasR was found, involving conserved residues from the ligand binding domain (LBD), beta turns in the short linker region (SLR) and the DNA-binding domain (DBD). This interaction is referred to as the LBD-SLR-DBD bridge or ‘the bridge’ interaction. Conclusions: This study may enable future experimental studies to detect the interaction of signalling molecules with “the bridge” of the LasR protein and suggests a potential new interaction site to assist antibacterial drug design.