1,721,061 research outputs found
Insight into the Mechanism of Hydrolysis of Meropenem by OXA-23 Serine-β-lactamase Gained by Quantum Mechanics/Molecular Mechanics Calculations
No full textThe fast and constant development of drug resistant bacteria represents a serious medical emergency. To overcome this problem, the development of drugs with new structures and modes of action is urgently needed. In this work, we investigated, at the atomistic level, the mechanisms of hydrolysis of Meropenem by OXA-23, a class D β-lactamase, combining unbiased classical molecular dynamics and umbrella sampling simulations with classical force field-based and quantum mechanics/molecular mechanics potentials. Our calculations provide a detailed structural and dynamic picture of the molecular steps leading to the formation of the Meropenem-OXA-23 covalent adduct, the subsequent hydrolysis, and the final release of the inactive antibiotic. In this mechanistic framework, the predicted activation energy is in good agreement with experimental kinetic measurements, validating the expected reaction path
Multidisciplinary strategy to investigate new lupin peptide inhibitors of PCSK9 activity as useful approach for cardiovascular disease risk reduction
No full textProprotein convertase subtilisin/kexin type 9 (PCSK9) has been recently identified as a new target for hypercholesterolemia treatment. The main role exploited by PCSK9 is the degradation of LDL receptor (LDLR) protein, leading to an increase of plasma cholesterol level. In this context, inhibition of PCSK9 is considered a good strategy for the treatment of hypercholesterolemia [1]. Recently, our research was focused mainly on lupin peptides, since in a recent paper it was shown that in hypercholesterolemic subjects, who had consumed dietary bars containing lupin protein for a month, the total cholesterol decrease was accompanied by a parallel decrement of circulating PCSK9 (-8.5%) versus the control group that had consumed casein bars [2]. For this reason, a multidisciplinary investigation was carried out in order to screen and develop new peptides, deriving from lupin protein hydrolysis and absorbable at intestinal level, which are able to modulate the PCSK9 target with a dual mechanism of action. More in details, lupin peptides reduce PCSK9 production and secretion through a decrease of HNF1-alpha in HepG2 cells and an absorbed lupin peptide, LILPKHSDAD (P5), is able to inhibit the protein-protein interaction (PPI) between PCSK9 and the LDLR with an IC50 value equal to 1.6±0.33 μM. In this context, a molecular docking analysis has allowed us to simulate the effects induced by P5 on the binding of PCSK9 to the LDLR (Figure 1. Simulation of the inhibitory binding of PCSK9 induced by P5). In fact, the superimposition of P5 on the EGF-A domain of LDLR co-crystallized with PCSK9 (PDB code 4NE9) showed a good overlapping, justifying the P5 inhibitory property
Biological Characterization of Computationally Designed Analogs of peptide TVFTSWEEYLDWV (Pep2-8) with Increased PCSK9 Antagonistic Activity
Full text linkThe inhibition of the PCSK9/LDLR protein-protein interaction (PPI) is a promising strategy for developing new hypocholesterolemic agents. Recently, new antibodies have been approved for therapy, but the high cost and low patients’ compliance stimulate the development of alternatives. Starting from the structural information available for the complex between PCSK9 and TVFTSWEEYLDWV (Pep2-8) peptide inhibitor and using computational methods, in this work we identified two Pep2-8 analogs as potential inhibitors of the PCSK9/LDLR PPI. Their biological characterization confirmed the theoretical outcomes. Remarkably, the treatment of HepG2 cells with these peptides increased the LDLR protein level on the cellular membrane, with activities that were 100 and 50 times better than the one of Pep2-8 tested at a 50 μM concentration. Moreover, they were 50 and 5 times more active than Pep2-8 in improving the functional ability of HepG2 cells to uptake extracellular LDL
Lupin peptides modulate the protein-protein interaction of PCSK9 with the low density lipoprotein receptor in HepG2 cells
Full text linkProprotein convertase subtilisin/kexin type 9 (PCSK9) has been recently identified as a new useful target for hypercholesterolemia treatment. This work demonstrates that natural peptides, deriving from the hydrolysis of lupin protein and absorbable at intestinal level, are able to inhibit the protein-protein interaction between PCSK9 and the low density lipoprotein receptor (LDLR). In order to sort out the best potential inhibitors among these peptides, a refined in silico model of the PCSK9/LDLR interaction was developed. Docking, molecular dynamics (MD) simulations and peptide binding energy estimations, by MM-GBSA approach, permitted to select the two best candidates among tested peptides that were synthesized and evaluated for their inhibitory activity. The most active was P5 that induced a concentration dependent inhibition of the PCSK9-LDLR binding, with an IC50 value equal to 1.6 ± 0.33 μM. Tested at a 10 μM concentration, this peptide increased by 66 ± 21.4% the ability of HepG2 cells to take up LDL from the extracellular environment
Orthosteric and allosteric ligands selectively acting at cholinergic receptor subtypes
No full textThe presentation will focus on the results recently achieved by our research group in the design, synthesis and pharmacological evaluation of selective ligands which target cholinergic receptor subtypes, belonging to both the nicotinic (nAChR) and the muscarinic (mAChR) acetylcholine receptor families. A set of spirocyclic derivatives will be illustrated, in which the simultaneous presence of the quinuclidinyl and Delta2-isoxazolinyl moieties, coupled with suitable stereoelectronic features of the substituent at position 3 of the spirocyclic ring, engendered a selective agonist profile at the homomeric neuronal alpha7 nAChRs [1]. The most promising compound in the series has been further investigated in preclinical studies and in in vivo models of CNS disorders and neuropathic pain. A group of novel hybrid peptides structurally related to natural alpha-conotoxins MII and PIA will be also presented, which behave as competitive antagonists able to discriminate alpha6beta2* and alpha3beta2* nAChR subtypes [2]. The five mAChR subtypes bind their physiological transmitter in the highly conserved orthosteric site within the transmembrane domains of the receptors. Orthosteric muscarinic agonists have negligible binding selectivity and poor signaling specificity. A less conserved allosteric site has been also characterized at the extracellular entrance of the binding pocket of mAChRs. To gain subtypeselective M2 receptor activation, we designed a group of putative bitopic compounds, i. e. hybrid derivatives fusing highly potent, unselective oxotremorinelike orthosteric activators with M2-selective bis(ammonio)alkane-type allosteric fragments. The new ligands interacted simultaneously with both recognition areas of the receptor protein, thus allowing the exploitation of favorable features of the orthosteric and the allosteric site by a single ligand molecule. The orthosteric interaction provided high affinity binding and activation of M2 mAChRs. The allosteric interaction yielded receptor subtype-selectivity and, in addition, could modulate efficacy and activate pathway-specific intracellular signaling [3]. [1] C.Dallanoce, P.Magrone, C.Matera, F.Frigerio, G.Grazioso, M.De Amici, S.Fucile, V.Piccari, K.Frydenvang, L.Pucci, C.Gotti, F.Clementi, C.De Micheli, ChemMedChem, 6, 2011, 889-903. [2] M.De Amici, G.Grazioso, C.Dallanoce, C.De Micheli et al., submitted. [3] K.Mohr, C.Tränkle, E.Kostenis, E.Barocelli, M.De Amici, U.Holzgrabe, Br.J.Pharmacol., 159, 2010, 997-1008
First Food-Derived Peptide Inhibitor of the Protein-Protein Interaction between Gain-of-Function PCSK9D374Y and the Low-Density Lipoprotein Receptor
No full textProprotein convertase subtilisin/kexin type 9 (PCSK9) is involved in cholesterol homeostasis, because it induces the low-density lipoprotein receptor (LDLR) degradation. This protein may carry some positive or negative mutations: PCSK9D374Y is one of the most dangerous gain-of-function mutations. This paper reports the identification of the first food-derived peptide able to inhibit the protein-protein interaction (PPI) between PCSK9D374Y and LDLR. In fact, T9 (GQEQSHQDEGVIVR), an absorbable peptide deriving from lupin β-conglutin, is able to impair the PPI between PCSK9D374Y and the LDLR, with an IC50 value equal to 285.6 ± 2.46 μM. The consequence of this inhibition is an increase of the protein level of the LDLR located on hepatic cell membranes up to 74.3 ± 4.4% and the restoration of the functional capability of HepG2 cells to uptake extracellular low-density lipoprotein up to 83.1 ± 1.6%. Finally, the putative binding mode of T9 to the LDLR binding site located on PCSK9D374Y was postulated by in silico tools
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
- …
