A bioinformatics search for selective histamine h4 receptor antagonists through structure-based virtual screening strategies

The prevalence of allergic disease is increasing dramatically in the developed world. Studies of allergic diseases have clearly demonstrated that histamine plays an important role in the pathogenesis of the early-phase allergic response. Histamine effects are mediated by H1, H2, H3, and H4 receptors. The presence of the histamine H4 receptors on leukocytes and mast cells suggests that the new histamine receptor H4 plays an important role in the modulation of the immune system. Thus, histamine H4 receptor is an attractive target for anti-allergic therapy. In our present study, we have generated a histamine H4 receptor model using I-TASSER based on human B2-adrenergic G-protein-coupled receptor. Structurally similar compounds of the three known antagonists JNJ777120, thioperamide, and Vuf6002 were retrieved from PubChem, and database was prepared. Virtual screening of those databases was performed, and six compounds with high docking score were identified. Also the binding mode revealed that all the six compounds had interaction with Asp94 of the receptor. Our results serve as a starting point in the development of novel lead compounds in anti-allergic therapy.     

Probing Secondary Glutaminyl Cyclase (QC) Inhibitor Interactions Applying an in silico‐Modeling/Site‐Directed Mutagenesis Approach: Implications for Drug Development

Glutaminyl cyclases (QCs) catalyze the formation of pyroglutamate‐modified amyloid peptides deposited in neurodegenerative disorders such as Alzheimer’s disease. Inhibitors of QC are currently in development as potential therapeutics. The crystal structures of the potent inhibitor PBD150 bound to human and murine QC (hQC, mQC) have been described recently. The binding modes of a dimethoxyphenyl moiety of the inhibitor are significantly different between the structures, which contrasts with a similar K_i value. We show the conformation of PBD150 prone to disturbance by protein–protein interactions within the crystals. Semi‐empirical calculations of the enzyme–inhibitor interaction within the crystal suggest significant differences in the dissociation constants between the binding modes. To probe for interactions in solution, a site‐directed mutagenesis on hQC was performed. The replacement of F325 and I303 by alanine or asparagine resulted in a 800‐fold lower activity of the inhibitor, whereas the exchange of S323 by alanine or valine led to a 20‐fold higher activity of PBD150. The results provide an example of deciphering the interaction mode between a target enzyme and lead substance in solution, if co‐crystallization does not mirror such interactions properly. Thus, the study might provide implications for rapid screening of binding modes also for other drug targets.     

Modulation of Opioid Receptor Ligand Affinity and Efficacy Using Active and Inactive State Receptor Models

Mu opioid receptor (MOR) agonists are widely used for the treatment of pain; however, chronic use results in the development of tolerance and dependence. It has been demonstrated that coadministration of a MOR agonist with a delta opioid receptor (DOR) antagonist maintains the analgesia associated with MOR agonists, but with reduced negative side‐effects. Using our newly refined opioid receptor models for structure‐based ligand design, we have synthesized several pentapeptides with tailored affinity and efficacy profiles. In particular, we have obtained pentapeptides 8 , Tyr‐c(S‐S)[DCys‐1Nal‐Nle‐Cys]NH₂, and 12 , Tyr‐c(S‐S)[DCys‐1Nal‐Nle‐Cys]OH, which demonstrates high affinity and full agonist behavior at MOR, high affinity but very low efficacy for DOR, and minimal affinity for the kappa opioid receptor (KOR). Functional properties of these peptides as MOR agonists/DOR antagonists lacking undesired KOR activity make them promising candidates for future in vivo studies of MOR/DOR interactions. Subtle structural variation of 12 , by substituting D‐Cys⁵ for L‐Cys⁵, generated analog 13, which maintains low nanomolar MOR and DOR affinity, but which displays no efficacy at either receptor. These results demonstrate the power and utility of accurate receptor models for structure‐based ligand design, as well as the profound sensitivity of ligand function on its structure.     

Characterization of diverse non-covalent interactions associated with protein acetylation

Protein acetylation has early emerged as a major posttranslational modification for histones and was recently found to be involved in a variety of biological events such as enzymatic activation and signal transduction. Traditional notion about the physicochemical effects associated with protein acetylation is mainly because of its presence capable of neutralizing positively charged protein system, while diverse non-covalent interactions arising from the acetylation are largely ignored and have never been investigated systematically. In the current work, we perform a comprehensive examination of the geometrical profile and energetic landscape of such acetylation-related non-covalent interactions in protein context by using a combination of high-level ab initio calculations, crystal structure survey, and hybrid mechanical/molecular mechanical analysis, on the basis of small model complexes and real protein systems. It is all coming together to suggest that the formation of complicated non-covalent networks around the acetylated site of protein is fundamentally important for stabilizing local structure, improving systemic rigidity, and even conducting more sophisticated biological functions such as switching enzymatic activity.     

3D-QSAR studies of JNK1 inhibitors utilizing various alignment methods

We report our three-dimensional quantitative structure activity relationship (3D-QSAR) studies of the series of anilinopyrimidine derivatives of JNK1 inhibitors. The comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were applied using different alignment methods. The ligand-based atom-by-atom matching alignment has produced better values for CoMFA (q(2) = 0.646 and r(2) = 0.983), while in CoMSIA it has achieved only lower statistical values. The pharmacophore-based model has produced (q(2) = 0.568, r(2) = 0.938) and (q(2) = 0.670, r(2) = 0.982) for CoMFA and CoMSIA models, respectively. As the model was based on the receptor-guided alignment, all the compounds were optimized within the receptor, resulting in q(2) = 0.605 and r(2) = 0.944 for CoMFA, and q(2) = 0.587 and r(2) = 0.863 for CoMSIA. Molecular Dynamic simulation studies suggested that the generated models were consistent with the low-energy protein ligand conformation. The CoMFA and CoMSIA contour maps indicated that the substitutions of the electropositive groups in the phenyl ring, and an addition of hydrophobic groups in the pyrimidine ring, are important to enhance the activity of this series. Moreover, the virtual screening analysis against NCI database yields potentials hits, and the results obtained would be useful to synthesize selective and highly potent c-Jun N-terminal kinase 1 analogs.     

The chemical tuning of a weak zinc binding motif for histone deacetylase using electronic effects

The hydroxamic acid moiety is an effective metal-binding warhead for a variety of metalloenzyme targets of interest in drug-discovery. For the zinc-containing histone deacetylase enzymes in particular, this chemical group has been widely incorporated and studied in the clinic. An alternative chemical functionality for binding zinc is the α-aminocarbonyl motif, which has been shown to bind to histone deacetylase enzymes. The current article explores the minimal binding site theoretical approach combined with structural knowledge to explore the ideal chemical substitution pattern of the α-aminocarbonyl motif within HDAC8. The metal-binding strength of the group is predicted to be highly tunable to chemical substitution at the carbonyl and the α-amino carbon. A fixed receptor model approach with a dispersion-corrected density functional, clearly discerned the effect of different substituents at both these positions using either a flexible or partially fixed ligand optimized in the presence of a fixed receptor model of the HDAC8 binding site. An electron donating substituent such as methyl at the C(α) in combination with NMe(2) substitution at the carbonyl position, similar to observed crystal structures, result in the optimal energetic profile for binding the zinc atom in the HDAC8 enzyme.     

Combined pharmacophore and 3D-QSAR study on a series of Staphylococcus aureus Sortase A inhibitors

Methicillin resistant Staphylococcus aureus has become a major health concern and it requires new therapeutic agents. Staphylococcus aureus Sortase A enzyme contributes in adherence of bacteria with the cell wall of host cell; consequently, inhibition of S. aureus Sortase A by small molecules could be employed as potential antibacterial agents against methicillin resistant S. aureus. Current study focused on the identification of 3D pharmacophoric features within a series of rhodanine, pyridazinone, and pyrazolethione analogs as S. aureus Sortase A inhibitors. Pharmacophore model was constructed employing representative molecules using Genetic Algorithm with Linear Assignment of Hypermolecular Alignment of Database. The identified pharmacophoric points were then utilized to create alignment hypothesis for three-dimensional quantitative structure-activity relationships. Outcome of comparative molecular field analysis and comparative molecular similarity indices analysis experiments were in good agreement (comparative molecular field analysis: q(2) = 0.562 and r(2) = 0.995, comparative molecular similarity indices analysis: q(2) = 0.549 and r(2) = 0.978) and capable of explaining the variance in biological activities coherently with respect to the structural features of compounds. The results were also found in concurrence with the outcome of pharmacophoric features.     

Time dependence of coupling in frequency-scaled bimanual coordination

Prior research has shown that fluctuations in the relative phase of bimanual coordination do not reflect a white Gaussian noise process. The present study furthered the examination of time-dependent properties in bimanual coordination by comparing the magnitude of relative phase variability and the degree of effector independence within the time domain. The original Kelso (1984) [10] bimanual frequency-scaling protocol was reproduced in which phase transitions from antiphase to in-phase were induced with increasing movement frequency. The results showed that as movement frequency was scaled-up the amount of relative phase variability increased and the effector movements became more dependent prior to the transition. This is consistent with previous modeling showing that stronger effector coupling can prevent the occurrence of phase transitions when long range correlations in relative phase are present. It appears that, as movement frequency is scaled up, increases in effector coupling strength minimize loss of pattern stability and delay the onset of phase transitions.     

Infection of primary human tonsillar lymphoid cells by KSHV reveals frequent but abortive infection of T cells

Insertion of nucleotide sequences encoding “tags” that can be expressed in specific viral proteins during an infection is a useful strategy for purifying viral proteins and their functional complexes from infected cells and/or for visualizing the dynamics of their subcellular location over time. To identify regions in the poliovirus polyprotein that could potentially accommodate insertion of tags, transposon-mediated insertion mutagenesis was applied to the entire nonstructural protein-coding region of the poliovirus genome, followed by selection of genomes capable of generating infectious, viable viruses. This procedure allowed us to identify at least one site in each viral nonstructural protein, except protein 2C, in which a minimum of five amino acids could be inserted. The distribution of these sites is analyzed from the perspective of their protein structural context and from the perspective of virus evolution.