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New small-size peptides modulators of the exosite of BACE1 obtained from a structure-based design. - Journal of biomolecular structure & dynamics
We report here two new small-size peptides acting as modulators of the BACE1 exosite. Ac-YPYFDPL-NH2 and Ac-YPYDIPL-NH2 displayed a moderated but significant inhibitory effect on BACE1. These peptides were obtained from a molecular modeling study. By combining MD simulations with ab initio and DFT calculations, a simple and generally applicable procedure to evaluate the binding energies of small-size peptides interacting with the exosite of the BACE1 is reported here. The structural aspects obtained for the different complexes were analyzed providing a clear picture about the binding interactions of these peptides. These interactions have been investigated within the framework of the density functional theory and the quantum theory of atoms in molecules (QTAIM) using a reduced model. Although the approach used here was traditionally applied to the study of non covalent interactions in small molecules complexes in gas phase, we show through in this work that this methodology is also a very powerful tool for the study of biomolecular complexes, providing a very detailed description of the binding event of peptides modulators at the exosite of BACE1.
Pentameric models as alternative molecular targets for the design of new antiaggregant agents. - Current protein & peptide science
The structure-based drug design has been an extremely useful technique used for searching and developing of new therapeutic agents in various biological systems. In the case of AD, this approach has been difficult to implement. Among other several causes, the main problem might be the lack of a specific stable and reliable molecular target. In this paper the results obtained using a pentameric amyloid beta (AÎ²) model as a molecular target are discussed. Our MD simulations have shown that this system is relatively structured and stable, displaying a lightly conformational flexibility during 2.0 Î¼s of simulation time. This study allowed us to distinguish characteristic structural features in specific regions of the pentamer which should be taken into account when choosing this model as a molecular target. This represents a clear advantage compared to the monomer or dimer models which are highly flexible structures with large numbers of possible conformers. Using this pentameric model we performed two types of studies usually carried out on a molecular target: a virtual screening and the design on structural basis of new mimetic peptides with antiaggregant properties. Our results indicate that this pentameric model might be a good molecular target for these particular studies of molecular modeling. Details about the predictive power of our virtual screening as well as about the molecular interactions that stabilize the mimetic peptide-pentamer AÎ² complexes are discussed in this paper.
Physical meaning of the QTAIM topological parameters in hydrogen bonding. - Journal of molecular modeling
This work examined the local topological parameters of charge density at the hydrogen bond (H-bond) critical points of a set of substituted formamide cyclic dimers and enolic tautomers. The analysis was performed not only on the total electron density of the hydrogen bonded complexes but also on the intermediate electron density differences derived from the Morokuma energy decomposition scheme. Through the connection between these intermediate electron density differences and the corresponding differences in topological parameters, the meaning of topological parameters variation due to hydrogen bonding (H-bonding) becomes evident. Thus, for example, we show in a plausible way that the potential energy density differences at the H-bond critical point properly describe the electrostatics of H-bonding, and local kinetic energy density differences account for the localization/delocalization degree of the electrons at that point. The results also support the idea that the total electronic energy density differences at the H-bond critical point describe the strength of the interaction rather than its covalent character as is commonly considered.
Autologous serum eye drops for dry eye. - The Cochrane database of systematic reviews
=Theoretically, autologous serum eye drops (AS) have a potential advantage over traditional therapies based on the assumption that ASserve not only as a lacrimal substitute to provide lubrication, but also contain other biochemical components mimicking natural tears more closely. The application of AS in dry eye treatment has gained popularity as a second-line therapy in the treatment of dry eye.Published studies on the subject indicate that autologous serum could be an effective treatment for dry eye.To evaluate the efficacy and safety of AS compared to artificial tears for treating dry eye.We searched CENTRAL (which contains the Cochrane Eyes and Vision Group Trials Register) (The Cochrane Library 2013, Issue 3),Ovid MEDLINE, Ovid MEDLINE In-Process and Other Non-Indexed Citations, Ovid MEDLINE Daily, Ovid OLDMEDLINE,(January 1950 to April 2013), EMBASE (January 1980 to April 2013), Latin American and Caribbean Literature on Health Sciences(LILACS) (January 1982 to April 2013), themetaRegister of Controlled Trials (mRCT) (www.controlled-trials.com), ClinicalTrials.gov(www.clinicaltrials.gov) and the WHO International Clinical Trials Registry Platform (ICTRP) (www.who.int/ictrp/search/en). We also searched the Science Citation Index Expanded database (September 2013) and reference lists of included studies. We did not use any date or language restrictions in the electronic searches for trials. We last searched the electronic databases on 15 April 2013.We included randomized controlled trials (RCTs) in which AS was compared to artificial tears in the treatment of dry eye in adults.Two review authors independently screened all titles and abstracts and assessed full-text articles of potentially eligible trials. Two review authors extracted data and assessed the methodological quality and characteristics of the included trials.We contacted investigators for missing data. For both primary and secondary outcomes, we reported mean differences with corresponding 95% confidence intervals(CIs) for continuous outcomes.We identified four eligible RCTs in which AS was compared with artificial tear treatment or saline in individuals (n = 72 participants)with dry eye of various etiologies (SjÃ¶grenâ€™s syndrome-related dry eye, non-SjÃ¶grenâ€™s syndrome dry eye and postoperative dry eye induced by laser-assisted in situ keratomileusis (LASIK)). The quality of the evidence provided by these trials was variable. A majority of the risk of bias domains were judged to have an unclear risk of bias in two trials owing to insufficient reporting of trial characteristics.One trial was considered to have a low risk of bias for most domains while another was considered to have a high risk of bias for most domains. Incomplete outcome reporting and heterogeneity in the participant populations and follow-up periods prevented the inclusion of these trials in a summary meta-analysis. For the primary outcome, improvement in participant-reported symptoms at one month, one trial (12 participants) showed no difference in participant-reported symptoms between 20% AS and artificial tears. Based on the results of two trials in 32 participants, 20% AS may provide some improvement in participant-reported symptoms compared to traditional artificial tears after two weeks of treatment. One trial also showed positive results with a mean difference in tear breakup time (TBUT) of 2.00 seconds (95% CI 0.99 to 3.01 seconds) between 20% AS and artificial tears after two weeks, which were not similar to findings from the other trials. Based on all other objective clinical assessments included in this review, AS was not associated with improvements in aqueous tear production measured by Schirmer's test (two trials, 33 participants), ocular surface condition with fluorescein (four trials, 72 participants) or Rose Bengal staining (three trials, 60 participants), and epithelial metaplasia by impression cytology compared to artificial tears (one trial, 12 participants). Data on adverse effects were not reported by three of the included studies. In one study, there were no serious adverse events reported with the collection of and treatment with AS.Overall there was inconsistency in the possible benefits of AS in improving participant-reported symptoms and TBUT and lack of effect based on other objective clinical measures. Well-planned, large, high-quality RCTs are warranted, in different severities of dry eye and using standardized questionnaires to measure participant-reported outcomes and objective clinical tests as well as objective biomarkers to assess the benefit of AS therapy for dry eye.
2,3,9- and 2,3,11-trisubstituted tetrahydroprotoberberines as D2 dopaminergic ligands. - European journal of medicinal chemistry
Dopamine-mediated neurotransmission plays an important role in relevant psychiatric and neurological disorders. Nowadays, there is an enormous interest in the development of new dopamine receptors (DR) acting drugs as potential new targets for the treatment of schizophrenia or Parkinson's disease. Previous studies have revealed that isoquinoline compounds such as tetrahydroisoquinolines (THIQs) and tetrahydroprotoberberines (THPBs) can behave as selective D2 dopaminergic alkaloids since they share structural similarities with dopamine. In the present study we have synthesized eleven 2,3,9- and 2,3,11-trisubstituted THPB compounds (six of them are described for the first time) and evaluated their potential dopaminergic activity. Binding studies on rat striatal membranes were used to evaluate their affinity and selectivity towards D1 and D2 DR and establish the structure-activity relationship (SAR) as dopaminergic agents. In general, all the tested THPBs with protected phenolic hydroxyls showed a lower affinity for D1 and D2 DR than their corresponding homologues with free hydroxyl groups. In previous studies in which dopaminergic affinity of 1-benzyl-THIQs (BTHIQs) was evaluated, the presence of a Cl into the A-ring resulted in increased affinity and selectivity towards D2 DR. This is in contrast with the current study since the existence of a chlorine atom into the A-ring of the THPBs caused increased affinity for D1 DR but dramatically reduced the selectivity for D2 DR. An OH group in position 9 of the THPB (9f) resulted in a higher affinity for DR than its homologue with an OH group in position 11 (9e) (250 fold for D2 DR). None of the compounds showed any cytotoxicity in freshly isolated human neutrophils. A molecular modelling study of three representative THPBs was carried out. The combination of MD simulations with DFT calculations provided a clear picture of the ligand binding interactions from a structural and energetic point of view. Therefore, it is likely that compound 9d (2,3,9-trihydroxy-THPB) behave as D2 DR agonist since serine residues cluster are crucial for agonist binding and receptor activation.Copyright Â© 2013 Elsevier Masson SAS. All rights reserved.
Molecular modeling study of dihydrofolate reductase inhibitors. Molecular dynamics simulations, quantum mechanical calculations, and experimental corroboration. - Journal of chemical information and modeling
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 ICâ‚…â‚€ 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.
Is the decrease of the total electron energy density a covalence indicator in hydrogen and halogen bonds? - Journal of molecular modeling
In this work, halogen bonding (XB) and hydrogen bonding (HB) complexes were studied with the aim of analyzing the variation of the total electronic energy density H(r b ) with the interaction strengthening. The calculations were performed at the MP2/6-311++G(2d,2p) level of approximation. To explain the nature of such interactions, the atoms in molecules theory (AIM) in conjunction with reduced variational space self-consistent field (RVS) energy decomposition analysis were carried out. Based on the local virial theorem, an equation to decompose the total electronic energy density H(r b ) in two energy densities, (-G(r b )) and 1/4âˆ‡(2)Ï(r b ), was derived. These energy densities were linked with the RVS interaction energy components. Through the connection between both decomposition schemes, it was possible to conclude that the decrease in H(r b ) with the interaction strengthening observed in the HB as well as the XB complexes, is mainly due to the increase in the attractive electrostatic part of the interaction energy and in lesser extent to the increase in its covalent character, as is commonly considered.
Searching the "biologically relevant"conformation of dopamine: a computational approach. - Journal of chemical information and modeling
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.
Expression of the SNAT2 amino acid transporter during the development of rat cerebral cortex. - International journal of developmental neuroscience : the official journal of the International Society for Developmental Neuroscience
The sodium-coupled neutral amino acid transporter 2 (SNAT2) is a protein that is expressed ubiquitously in mammalian tissues and that displays Na(+), voltage and pH dependent activity. This transporter mediates the passage of small zwitterionic amino acids across the cell membrane and regulates the cell homeostasis and its volume. We have examined the expression of SNAT2 mRNA and protein during the development of the rat cerebral cortex, from gestation through the postnatal stages to adulthood. Our data reveal that SNAT2 mRNA and protein expression is higher during embryogenesis, while it subsequently diminishes during postnatal development. Moreover, during embryonic period SNAT2 colocalizes with the radial glial cells marker GLAST, while in postnatal period it is mainly detected in neuronal dendrites. These findings suggest a relevant role for amino acid transport through SNAT2 in the developing embryonic brain.Copyright Â© 2011 ISDN. Published by Elsevier Ltd. All rights reserved.
Strength and nature of hydrogen bonding interactions in mono- and di-hydrated formamide complexes. - The journal of physical chemistry. A
In this work, mono- and di-hydrated complexes of the formamide were studied. The calculations were performed at the MP2/6-311++G(d,p) level of approximation. The atoms in molecules theory (AIM), based on the topological properties of the electronic density distribution, was used to characterize the different types of bonds. The analysis of the hydrogen bonds (H-bonds) in the most stable mono- and di-hydrated formamide complexes shows a mutual reinforcement of the interactions, and some of these complexes can be considered as "bifunctional hydrogen bonding hydration complexes". In addition, we analyzed how the strength and the nature of the interactions, in mono-hydrated complexes, are modified by the presence of a second water molecule in di-hydrated formamide complexes. Structural changes, cooperativity, and electron density redistributions demonstrate that the H-bonds are stronger in the di-hydrated complexes than in the corresponding mono-hydrated complexes, wherein the Ïƒ- and Ï€-electron delocalization were found. To explain the nature of such interactions, we carried out the atoms in molecules theory in conjunction with reduced variational space self-consistent field (RVS) decomposition analysis. On the basis of the local Virial theorem, the characteristics of the local electron energy density components at the bond critical points (BCPs) (the 1/4âˆ‡ (2)Ï(b) component of electron energy density and the kinetic energy density) were analyzed. These parameters were used in conjunction with the electron density and the Laplacian of the electron density to analyze the characteristics of the interactions. The analysis of the interaction energy components for the systems considered indicates that the strengthening of the hydrogen bonds is manifested by an increased contribution of the electrostatic energy component represented by the kinetic energy density at the BCP.
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