An inhibitory mechanism of action of coiled-coil peptides against type three secretion system from enteropathogenic Escherichia coli.

Human pathogenic gram-negative bacteria, such as enteropathogenic Escherichia coli (EPEC), rely on type III secretion systems (T3SS) to translocate virulence factors directly into host cells. The coiled-coil domains present in the structural proteins of T3SS are conformed by amphipathic alpha-helical structures that play an important role in the protein-protein interaction and are essential for the assembly of the translocation complex. To investigate the inhibitory capacity of these domains on the T3SS of EPEC, we synthesized peptides between 7 and 34 amino acids based on the coiled-coil domains of proteins that make up this secretion system. This analysis was performed through in vitro hemolysis assays by assessing the reduction of T3SS-dependent red blood cell lysis in the presence of the synthesized peptides. After confirming its inhibitory capacity, we performed molecular modeling assays using combined techniques, docking-molecular dynamic simulations, and quantum-mechanic calculations of the various peptide-protein complexes, to improve the affinity of the peptides to the target proteins selected from T3SS. These techniques allowed us to demonstrate that the peptides with greater inhibitory activity, directed against the coiled-coil domain of the C-terminal region of EspA, present favorable hydrophobic and hydrogen bond molecular interactions. Particularly, the hydrogen bond component is responsible for the stabilization of the peptide-protein complex. This study demonstrates that compounds targeting T3SS from pathogenic bacteria can indeed inhibit bacterial infection by presenting a higher specificity than broad-spectrum antibiotics. In turn, these peptides could be taken as initial structures to design and synthesize new compounds that mimic their inhibitory pharmacophoric pattern.

Polycerasoidol, a Natural Prenylated Benzopyran with a Dual PPARα/PPARγ Agonist Activity and Anti-inflammatory Effect.

Dual peroxisome proliferator-activated receptor-α/γ (PPARα/γ) agonists regulate both lipid and glucose homeostasis under different metabolic conditions and can exert anti-inflammatory activity. We investigated the potential dual PPARα/γ agonism of prenylated benzopyrans polycerasoidol (1) and polycerasoidin (2) and their derivatives for novel drug development. Nine semisynthetic derivatives were prepared from the natural polycerasoidol (1) and polycerasoidin (2), which were evaluated for PPARα, -γ, -δ and retinoid X receptor-α activity in transactivation assays. Polycerasoidol (1) exhibited potent dual PPARα/γ agonism and low cytotoxicity. Structure-activity relationship studies revealed that a free phenol group at C-6 and a carboxylic acid at C-9' were key features for dual PPARα/γ agonism activity. Molecular modeling indicated the relevance of these groups for optimal ligand binding to the PPARα and PPARγ domains. In addition, polycerasoidol (1) exhibited a potent anti-inflammatory effect by inhibiting mononuclear leukocyte adhesion to the dysfunctional endothelium in a concentration-dependent manner via RXRα/PPARγ interactions. Therefore, polycerasoidol (1) can be considered a hit-to-lead molecule for the further development of novel dual PPARα/γ agonists capable of preventing cardiovascular events associated with metabolic disorders.

Alkaloids from Hippeastrum argentinum and Their Cholinesterase-Inhibitory Activities: An in Vitro and in Silico Study.

Two new alkaloids, 4-O-methylnangustine (1) and 7-hydroxyclivonine (2) (montanine and homolycorine types, respectively), and four known alkaloids were isolated from the bulbs of Hippeastrum argentinum, and their cholinesterase-inhibitory activities were evaluated. These compounds were identified using GC-MS, and their structures were defined by physical data analysis. Compound 2 showed weak butyrylcholinesterase (BuChE)-inhibitory activity, with a half-maximal inhibitory concentration (IC50) value of 67.3 ± 0.09 µM. To better understand the experimental results, a molecular modeling study was also performed. The combination of a docking study, molecular dynamics simulations, and quantum theory of atoms in molecules calculations provides new insight into the molecular interactions of compound 2 with BuChE, which were compared to those of galantamine.

Molecular modeling study of dihydrofolate reductase inhibitors. Molecular dynamics simulations, quantum mechanical calculations, and experimental corroboration.

A molecular modeling study on dihydrofolate reductase (DHFR) inhibitors was carried out. By combining molecular dynamics simulations with semiempirical (PM6), ab initio, and density functional theory (DFT) calculations, a simple and generally applicable procedure to evaluate the binding energies of DHFR inhibitors interacting with the human enzyme is reported here, providing a clear picture of the binding interactions of these ligands from both structural and energetic viewpoints. A reduced model for the binding pocket was used. This approach allows us to perform more accurate quantum mechanical calculations as well as to obtain a detailed electronic analysis using the quantum theory of atoms in molecules (QTAIM) technique. Thus, molecular aspects of the binding interactions between inhibitors and the DHFR are discussed in detail. A significant correlation between binding energies obtained from DFT calculations and experimental IC50 values was obtained, predicting with an acceptable qualitative accuracy the potential inhibitor effect of nonsynthesized compounds. Such correlation was experimentally corroborated synthesizing and testing two new inhibitors reported in this paper.

Searching the "biologically relevant"conformation of dopamine: a computational approach.

We report here an exhaustive and complete conformational study on the conformational potential energy hypersurface (PEHS) of dopamine (DA) interacting with the dopamine D2 receptor (D2-DR). A reduced 3D model for the binding pocket of the human D2-DR was constructed on the basis of the theoretical model structure of bacteriorhodopsin. In our reduced model system, only 13 amino acids were included to perform the quantum mechanics calculations. To obtain the different complexes of DA/D2-DR, we combined semiempirical (PM6), DFT (B3LYP/6-31G(d)), and QTAIM calculations. The molecular flexibility of DA interacting with the D2-DR was evaluated from potential energy surfaces and potential energy curves. A comparative study between the molecular flexibility of DA in the gas phase and at D2-DR was carried out. In addition, several molecular dynamics simulations were carried out to evaluate the molecular flexibility of the different complexes obtained. Our results allow us to postulate the complexes of type A as the "biologically relevant conformations" of DA. In addition, the theoretical calculations reported here suggested that a mechanistic stepwise process takes place for DA in which the protonated nitrogen group (in any conformation) acts as the anchoring portion, and this process is followed by a rapid rearrangement of the conformation allowing the interaction of the catecholic OH groups.

Ab initio and DFT study of the conformational energy hypersurface of cyclic Gly-Gly-Gly.

The multidimensional conformational potential energy hypersurface (PEHS) of cyclic Gly-Gly-Gly (1,4,7-triazonane-2,5,8-trione) was comprehensively investigated at the Hartree-Fock (RHF/6-31G(d)) level of theory. The equilibrium structures, their relative stability, and the transition state (TS) structures involved in the conformational interconversion pathways were analyzed. aug-cc-pVTZ//B3LYP/6-311++G** single point calculations predict a trans-cis-cis conformation as the energetically preferred form for this compound. However, all of the levels of theory employed here predicted that two forms, a trans-cis-cis and a cis-cis-cis (crown), of conformers contribute significantly to the equilibrium mixture at room temperature. The conformational interconversion between the global minimum and the symmetric cis-cis-cis crown form requires 12.49 kcal/mol at the RHF 6-31G(d) level of theory, whereas the conformational interconversion between the cis-cis-cis crown and cis-cis-cis boat form requires 18.70 kcal/mol. An exploratory topological analysis of the PEHS was also carried out. Our results allow us to form a concise idea about the internal intricacies of the PEHSs of these cyclic tripeptides, describing the conformations as well as the conformational interconversion processes in these hypersurfaces.

Synthesis, dopaminergic profile, and molecular dynamics calculations of N-aralkyl substituted 2-aminoindans.

Brain dopaminergic system has a crucial role in the etiology of several neuropsychiatric disorders, including Parkinson's disease, depression, and schizophrenia. Several dopaminergic drugs are used to treat these pathologies, but many problems are attributed to these therapies. Within this context, the search for new more efficient dopaminergic agents with less adverse effects represents a vast research field. The aim of the present study was to synthesize N-[2-(4,5-dihydroxyphenyl)-methyl-ethyl]-4,5-dihydroxy-2-aminoindan hydrobromide (3), planned to be a dopamine ligand, and to evaluate its dopaminergic action profile. This compound was assayed as a diastereoisomeric mixture in two experimental models: stereotyped behavior (gnaw) and renal urinary response, after central administration. The pharmacological results showed that compound 3 significantly blocked the apomorphine-induced stereotypy and dopamine-induced diuresis and natriuresis in rats. Thus, compound 3 demonstrated an inhibitory effect on dopaminergic-induced behavior and renal action. N-[2-(-Methyl-ethyl)]-4,5-dihydroxy-2-aminoindan hydrobromide (4) was previously reported as an inotropic agent, and in the present work it was also re-evaluated as a diastereoisomeric mixture for its possible central action on the behavior parameters such as stereotypy and dopamine-induced diuresis and natriuresis in rats. Our results indicate that compound 4 produces an agonistic response, possibly through dopaminergic mechanisms. To better understand the experimental results we performed molecular dynamics simulations of two complexes: compound 3/D(2)DAR (dopamine receptor) and compound 4/D(2)DAR. The differential binding mode obtained for these complexes could explain the antagonist and agonist activity obtained for compounds 3 and 4, respectively.

Ring inversion in 1,4,7 cyclononatriene and analogues: Ab initio and DFT calculations and topological analysis.

The multidimensional conformational potential energy hypersurfaces (PEHSs) for cis-cis-cis 1,4,7 cyclononatriene (I), Tribenzocyclononatriene (TBCN) (II), and cis-cis-cis cyclic triglycine (III) were comprehensively investigated at the Hartree-Fock (HF/6-31G(d)) and density functional theory (B3LYP/6-31G(d,p)) levels of theory. The equilibrium structures, their relative stability, and the transition state (TS) structures involved in the conformational interconversion pathways were analyzed. Altogether, four geometries (two low-energy conformations and two transition states) were found to be important for a description of the conformational features of compounds I-III. B3LYP/aug-cc-pvdz//B3lYP/6-31G(d,p) and MP2/6-31G(d,p)//B3LYP/6-31G(d,p) single point calculations predict that the conformational interconversion between crown and twist forms requires 14.01, 26.71, and 17.79 kcal/mol for compounds I, II, and III, respectively, which is in agreement with the available experimental data. A topological study of the conformational PEHSs of compounds I-III was performed. Our results allow us to form a concise idea about the internal intricacies of the PEHSs of compounds I-III, describing the conformations as well as the conformational interconversion process in these hypersurfaces.

Dynamics of flexible cycloalkanes. Ab initio and DFT study of the conformational energy hypersurface of cyclononane.

The multidimensional Potential Energy Hypersurface (PEHS) for the cyclononane molecule was comprehensively investigated at the Hartree-Fock (HF), and Density Functional Theory (DFT) levels of theory. Second-order Møller-Plesset perturbation theory (MP2) optimizations were also carried out to confirm the low-energy conformations. The previously reported Geometrical Algorithm to Search Conformational Space (GASCOS) has been used to generate the starting geometries for the conformational analysis. The GASCOS algorithm combined with ab initio and DFT optimization permits searching of the potential energy hypersurface for all minimum-energy conformations as well as transition structures connecting the low-energy forms. The search located all previously reported structures together with 11 transition states, some of which were not found by earlier searching techniques. Altogether, 16 geometries (five low-energy conformations and 11 transition states) were found to be important for a description of the conformational features of cyclononane. RB3LYP/aug-cc-pVTZ//RB3LYP/6-31G(d) calculations suggest a conformational mixture between the twist boat-chair and twist chair-boat conformations as the preferred forms. In addition only the twist chair-chair conformation with 1.52 kcal/mol above the global minimum should contribute somewhat to the equilibrium mixture of conformations. Our results allow us to form a concise idea about the internal intricacies of the 9D vector space describing the conformation of cyclononane as well as the associated conformational potential energy hypersurface of nine independent variables.

Structure-activity relationship study of homoallylamines and related derivatives acting as antifungal agents.

The synthesis, in vitro evaluation, and structure-activity relationship studies of homoallylamines and related derivatives acting as antifungal agents are reported. Among them, compounds N-(4-bromophenyl)-N-(2-furylmethyl)amine and N-(4-chlorophenyl)-N-(2-furylmethyl)amine reported here exhibited remarkable antifungal activity against dermatophytes. Theoretical calculations allow us to determine the minimal structural requirements to produce the antifungal response and can provide a guide for the design of compounds with these properties.