Homology modelling of a sensor histidine kinase from Aeromonas hydrophila

Virtual Screening Uncovers DspS Activators That Disperse Pseudomonas aeruginosa Biofilms

Pseudomonas aeruginosa is the predominant bacterium found in many chronic biofilm infections. Over the past few decades, biofilm-related infections have posed a significant challenge to medical practice due to the increasing emergence of multidrug resistance. Cis-2-decenoic acid (CDA), a small molecule found in P. aeruginosa, has been shown to disperse biofilms formed by various bacteria and to work in synergy with common antibiotics. Despite that, the binding mechanism between CDA and the predicted cyclases/histidine kinases associated sensory extracellular (CHASE) domain of sensor protein DspS remains unknown in the absence of a crystallized protein structure. Moreover, the therapeutic potential of CDA is limited by its susceptibility to oxidative degradation and isomerization. In this work, we propose a structural model for the DspS CHASE domain. The resulting model displays an overall topology reminiscent of the sensor protein PcrK in Xanthomonas campestris. Through molecular dynamics simulations, a stable potential binding site for CDA was further identified. Virtual screening against the predicted site of DspS CHASE using our developed pipeline discovered two promising compounds, compounds 2 and 9, capable of dislodging 7-day P. aeruginosa biofilms at 50 μM without affecting bacterial growth. These compounds also enhanced the effects of ciprofloxacin against P. aeruginosa, reduced the survival of dispersed cells, and increased the expression of matrix-degrading enzyme genes pelA, pslG, and eddA. This study provides insights into CDA recognition by DspS and represents the first large-scale effort to uncover first-in-class DspS activators. At the same time, this work also underscores the effectiveness of a computational-aided drug discovery process in finding new activators, even without a known protein structure.

Molecular characterization and interactome analysis of aerolysin (aer) gene from fish pathogen Aeromonas veronii: The pathogenicity inferred from sequence divergence and linked to histidine kinase (cheA)

Aerolysin (aer) is one of the most important and abundant virulence factors in the infection of fish by Aeromonas veronii. A comprehensive study on the molecular characterization and pathogenicity of the aer gene from 34 A. veronii isolates from diseased carp and catfish was carried out and its interactome was analysed to observe the functional correlations between aer and other proteins within the A. veronii network. The PCR-based amplification of aer from the 34 isolates of A. veronii showed more aer-positive isolates from catfish with a high pathogenic potential in the in vivo challenge test than the carp fish. The analysis of aer gene sequence from challenged fish revealed significant sequence divergence according to the types and geographical distribution of the fish. The networking analysis of aer from the model A. veronii B565 revealed histidine kinase (cheA) as the most functional interacting partner. The study of the interaction between aer from the experimental A. veronii and cheA demonstrated that the A chain of cheA plays a more important role than the corresponding B chain during contact, and a linker sequence of 15 residues controlled the entire interaction process. Therefore, cheA could be an excellent drug target for controlling A. veronii infection of fish.

Toward a better understanding of the interaction between somatostatin receptor 2 and its ligands: a structural characterization study using molecular dynamics and conceptual density functional theory

This study is a part of the extensive research intending to provide the structural insights on somatostatin and its receptor. Herein, we have studied the structural complexity involved in the binding of somatostatin receptor 2 (SSTR2) with its agonists and antagonist. A 3D QSAR study based on comparative molecular field analysis and comparative molecular similarity analysis (CoMSIA) discerned that a SSTR2 ligand with electronegative, less-bulkier, and hydrogen atom donating/accepting substitutions is important for their biological activity. A conceptual density functional theory (DFT) study was followed to study the chemical behavior of the ligands based on the molecular descriptors derived using the Fukui's molecular orbital theory. We have performed molecular dynamics simulations of receptor-ligand complexes for 100 ns to analyze the dynamic stability of the backbone Cα atoms of the receptor and strength and approachability of the receptor-ligand complex. The findings of this study could be efficacious in the further studies understanding intricate structural features of the somatostatin receptors and in discovering novel subtype-specific ligands with higher affinity. Communicated by Ramaswamy H. Sarma.

Isolation, purification and characterization of proteinaceous fungal α-amylase inhibitor from rhizome of Cheilocostus speciosus (J.Koenig) C.D.Specht

As the aim of this present study, a proteinaceous α-amylase inhibitor has been isolated from the rhizome of Cheilocostus specious (C. speciosus) and was purified using DEAE cellulose anion exchange chromatography followed by gel filtration using Sephacryl-S-200 column. The purity and molecular mass of the purified inhibitor was determined by SDS-PAGE and LC-MS respectively. The molecular mass of the purified inhibitor was determined to be 31.18kDa. Protein-protein docking was also carried out as molecular model. Model validation methods such as Ramachandran plot and Z-score plot were adopted to validate the structural description (sequence analysis) of proteins. The inhibitory activity was confirmed using spectrophotometric and reverse zymogram analyses. This 31.18kDa protein from C. speciosus inhibited the activity of fungal α-amylase by 71% at the level of ion exchange chromatography and 96% after gel filtration. The inhibition activity of the α-amylase inhibitor was stable and high at optimum pH6 (52.2%) and temperatures of 30-40°C (72.2%). Thus it was suggested that the main responsible for the versatile biological and pharmacological activities of C. speciosus is due to its primary metabolites (proteins) only.

Theoretical analysis of somatostatin receptor 5 with antagonists and agonists for the treatment of neuroendocrine tumors

We report on SSTR5 receptor modeling and its interaction with reported antagonist and agonist molecules. Modeling of the SSTR5 receptor was carried out using multiple templates with the aim of improving the precision of the generated models. The selective SSTR5 antagonists, agonists and native somatostatin SRIF-14 were employed to propose the binding site of SSTR5 and to identify the critical residues involved in the interaction of the receptor with other molecules. Residues Q2.63, D3.32, Q3.36, C186, Y7.34 and Y7.42 were found to be highly significant for their strong interaction with the receptor. SSTR5 antagonists were utilized to perform a 3D quantitative structure-activity relationship study. A comparative molecular field analysis (CoMFA) was conducted using two different alignment schemes, namely the ligand-based and receptor-based alignment methods. The best statistical results were obtained for ligand-based ([Formula: see text], [Formula: see text] = 0.988, noc = 4) and receptor-guided methods (docked mode 1:[Formula: see text], [Formula: see text], noc = 5), (docked mode 2:[Formula: see text] = 0.555, [Formula: see text], noc = 5). Based on CoMFA contour maps, an electropositive substitution at [Formula: see text], [Formula: see text] and [Formula: see text] position and bulky group at [Formula: see text] position are important in enhancing molecular activity.

Theoretical analysis of somatostatin receptor 5 with antagonists and agonists for the treatment of neuroendocrine tumors

We report on SSTR5 receptor modeling and its interaction with reported antagonist and agonist molecules. Modeling of the SSTR5 receptor was carried out using multiple templates with the aim of improving the precision of the generated models. The selective SSTR5 antagonists, agonists and native somatostatin SRIF-14 were employed to propose the binding site of SSTR5 and to identify the critical residues involved in the interaction of the receptor with other molecules. Residues Q2.63, D3.32, Q3.36, C186, Y7.34 and Y7.42 were found to be highly significant for their strong interaction with the receptor. SSTR5 antagonists were utilized to perform a 3D quantitative structure-activity relationship study. A comparative molecular field analysis (CoMFA) was conducted using two different alignment schemes, namely the ligand-based and receptor-based alignment methods. The best statistical results were obtained for ligand-based ([Formula: see text], [Formula: see text] = 0.988, noc = 4) and receptor-guided methods (docked mode 1:[Formula: see text], [Formula: see text], noc = 5), (docked mode 2:[Formula: see text] = 0.555, [Formula: see text], noc = 5). Based on CoMFA contour maps, an electropositive substitution at [Formula: see text], [Formula: see text] and [Formula: see text] position and bulky group at [Formula: see text] position are important in enhancing molecular activity.

Clostridium-DT(DB): a comprehensive database for potential drug targets of Clostridium difficile

Clostridium difficile is considered to be one of the most important causes of health care-associated infections currently. The prevalence and severity of C. difficile infection have increased significantly worldwide in the past decade which has led to the increased research interest. Here, using comparative genomics strategy coupled with bioinformatics tools we have identified potential drug targets in C. difficile and determined their three-dimensional structures in order to develop a database, named Clostridium-DT(DB). Currently, the database comprises the potential drug targets with their structural information from three strains of C. difficile, namely hypervirulent PCR-ribotype 027 strain R20291, PCR-ribotype 012 strain 630, and PCR-ribotype 027 strain CD196.