Design and SAR Analysis of Covalent Inhibitors Driven by Hybrid QM/MM Simulations

Quantum mechanics/molecular mechanics (QM/MM) hybrid technique is emerging as a reliable computational method to investigate and characterize chemical reactions occurring in enzymes. From a drug discovery perspective, a thorough understanding of enzyme catalysis appears pivotal to assist the design of inhibitors able to covalently bind one of the residues belonging to the enzyme catalytic machinery. Thanks to the current advances in computer power, and the availability of more efficient algorithms for QM-based simulations, the use of QM/MM methodology is becoming a viable option in the field of covalent inhibitor design. In the present review, we summarized our experience in the field of QM/MM simulations applied to drug design problems which involved the optimization of agents working on two well-known drug targets, namely fatty acid amide hydrolase (FAAH) and epidermal growth factor receptor (EGFR). In this context, QM/MM simulations gave valuable information in terms of geometry (i.e., of transition states and metastable intermediates) and reaction energetics that allowed to correctly predict inhibitor binding orientation and substituent effect on enzyme inhibition. What is more, enzyme reaction modelling with QM/MM provided insights that were translated into the synthesis of new covalent inhibitor featured by a unique combination of intrinsic reactivity, on-target activity, and selectivity

Investigación arqueométrica de los ladrillos de las antiguas murallas defensivas de la ciudad de Pavía (norte de Italia)

A study was conducted on bricks sampled from the defense walls around the historic town of Pavia (northern Italy) erected during Roman (uncertain) and “Spanish”(sixteenth-seventeenth centuries) times. An analysis of colour, macro- and micro-chemical composition,mineralogical clusters and structural-textural features showed that similar raw materials were used in the manufacture of these bricks, although certain variations were identified: particle size is finer in Roman bricks, while the “Spanish” version contains ground carbonate and “chamotte” additives. The “Spanish” bricks,fired at lower temperatures, are more porous. The wide range of firing temperatures used to make “Spanish” bricks was very likely related to the intended use. The sporadic presence of maghemite is discussed in the context of the atmosphere prevailing in the kilns. The “Spanish” bricks are lighter in colour as a result of their carbonate content and lower firing temperature. These characteristics, which affect the weather resistance of the different types of brick, should be taken into account in restoration work.Se investigan ladrillos recogidos en las murallas defensivas de la histórica ciudad de Pavía (norte de Italia), que fueron construidas en tiempos romanos (no establecidos)y “españoles” (siglos XVI y XVII).En base al color, composición química tanto total como puntual, asociaciones mineralógicas y características texturales,se concluye que se utilizó una materia prima similar en ambas épocas, con algunas particularidades: granulometría más fina en los romanos, adición de carbonato molido y chamota en los “españoles”. Por su parte, la porosidad es mayor en los ladrillos “españoles”. El amplio rango de temperaturas de cocción observado para estos últimos debe estar relacionado con los distintos usos para los cuales fueron destinados. La presencia esporádica de maghemita se discute, además, en función del tipo de atmósfera imperante en el horno de cocción. El color de los ladrillos “españoles” es más claro, como corresponde a su mayor contenido en carbonatos y menor temperatura de cocción. Estas características ejercen una notable influencia en la resistencia a la meteorización de los distintos tipos de ladrillos y deben, ser tenidas en cuenta ala hora de elaborar posibles planes de restauración

N-Acylethanolamine Acid Amidase (NAAA): Mechanism of Palmitoylethanolamide Hydrolysis Revealed by Mechanistic Simulations

The N-terminal cysteine hydrolase N-acylethanolamine acid amidase (NAAA) catalyzes the hydrolytic deactivation of the lipid messenger palmitoylethanolamide (PEA), with optimal activity at acidic pH. Using the crystal structure of human NAAA as a starting point, we investigated the catalytic mechanism of PEA hydrolysis with a multiscale approach based on classic molecular dynamics (MD) and quantum mechanical/molecular mechanics (QM/MM) simulations coupled with enhanced sampling and path-collective variables (PCVs). The proton configuration of the catalytic nucleophile, Cys126, and of the surrounding carboxylates was critical to preserve the active site architecture. A stable Michaelis complex was then used to reconstruct the free-energy surfaces of NAAA acylation and deacylation during PEA hydrolysis. Acylation emerged as the critical step, with Cys126 acting both as an acid, to protonate the ethanolamine leaving group, and as a nucleophile, to attack the PEA carbonyl carbon. The ethanol fragment of PEA did not appear to play an indispensable role in acylation, a result further supported by kinetic experiments showing that NAAA hydrolyzes palmitoyl methyl amide (PMA) with high catalytic efficiency. Our multiscale approach identified a distinctive protonation state and catalytic mechanism for NAAA which accounts for pH-dependent activity, mutagenesis data, and mechanism of covalent inhibitors

Micro- and Nanopatterned Silk Substrates for Antifouling Applications

A major problem of current biomedical implants is the bacterial colonization and subsequent biofilm formation, which seriously affects their functioning and can lead to serious post-surgical complications. Intensive efforts have been directed toward the development of novel technologies that can prevent bacterial colonization while requiring minimal antibiotics doses. To this end, biocompatible materials with intrinsic antifouling capabilities are in high demand. Silk fibroin, widely employed in biotechnology, represents an interesting candidate. Here, we employ a soft-lithography approach to realize micro- and nanostructured silk fibroin substrates, with different geometries. We show that patterned silk film substrates support mammal cells (HEK-293) adhesion and proliferation, and at the same time, they intrinsically display remarkable antifouling properties. We employ Escherichia coli as representative Gram-negative bacteria, and we observe an up to 66% decrease in the number of bacteria that adhere to patterned silk surfaces as compared to control, flat silk samples. The mechanism leading to the inhibition of biofilm formation critically depends on the microstructure geometry, involving both a steric and a hydrophobic effect. We also couple silk fibroin patterned films to a biocompatible, optically responsive organic semiconductor, and we verify that the antifouling properties are very well preserved. The technology described here is of interest for the next generation of biomedical implants, involving the use of materials with enhanced antibacterial capability, easy processability, high biocompatibility, and prompt availability for coupling with photoimaging and photodetection techniques

Procesos de alteración asociados al contenido de minerales arcillosos en materiales pétreos

Stone alterability/durability is depending upon a number of intrinsic and extrinsic factors among which "clay minerals" constituents, either diffused throughout the stone framework or as coating-filling of void spaces, can play an important role. Swelling-shrinking and aggregation-disaggregation phenomena occurring by interaction of argillaceous particles with water and other fluids can cause destructuration of the stone resulting in a variety of pathologies. Also salt crystallization which is depending on fluid transfer, moisture evaporation and ion concentration in the circulating solutions, can be influenced by clay mineral reactivity. Furthermore, saline solutions can drastically change the clay minerals behaviour, resulting in enhanced "osmotic" swelling and variations in clay aggregation geometry; these phenomena resulting in significant stone damage. Case histories concerning several lithotypes used for monumental buildings and artistic manufacts are reported for showing the role of different clay mineral types in determining trend and intensity of decay processes.Varios factores, tanto intrínsecos como extrínsecos, pueden condicionar la alterabilidad/durabilidad de materiales pétreos. Entre ellos, la presencia de minerales arcillosos, bien como constituyentes difusos o recubriendo-rellenando huecos, puede jugar un papel importante. El resultado de la interacción de las partículas arcillosas y el agua (u otros fluidos) da lugar a patologías que son consecuencia de una serie de daños internos producidos por las continuas variaciones plásticas, asociadas a parámetros físicos y cristaloquímicos de este tipo de minerales. Entre los que podemos citar la desestructuración de la piedra (bien por agregación-desagregación de las partículas arcillosas o por procesos de hinchamiento-contracción) que está asociado, por ejemplo, con la cristalización de sales, producida por la transferencia de fluidos a su través, o a variaciones de humedad, a concentraciones iónicas de la solución, en función de la reactividad de las arcillas presentes, o a efectos provocados por tensiones osmóticas que modifican la geometría de aglutinación de las propias partículas. En este artículo se analizan diferentes litotipos utilizados en la construcción y ornamentación de edificios históricos, todos ellos con minerales arcillosos, así como sus patologías, definiéndose las tendencias y los procesos degradativos encontrados

Calcium as a key player in arrhythmogenic cardiomiopathy : adhesion disorder or intracellular alteration?

Arrhythmogenic cardiomyopathy (ACM) is an inherited heart disease characterized by sudden death in young people and featured by fibro-adipose myocardium replacement, malignant arrhythmias, and heart failure. To date, no etiological therapies are available. Mutations in desmosomal genes cause abnormal mechanical coupling, trigger pro-apoptotic signaling pathways, and induce fibro-adipose replacement. Here, we discuss the hypothesis that the ACM causative mechanism involves a defect in the expression and/or activity of the cardiac Ca2+ handling machinery, focusing on the available data supporting this hypothesis. The Ca2+ toolkit is heavily remodeled in cardiomyocytes derived from a mouse model of ACM defective of the desmosomal protein plakophilin-2. Furthermore, ACM-related mutations were found in genes encoding for proteins involved in excitation\u2012contraction coupling, e.g., type 2 ryanodine receptor and phospholamban. As a consequence, the sarcoplasmic reticulum becomes more eager to release Ca2+, thereby inducing delayed afterdepolarizations and impairing cardiac contractility. These data are supported by preliminary observations from patient induced pluripotent stem-cell-derived cardiomyocytes. Assessing the involvement of Ca2+ signaling in the pathogenesis of ACM could be beneficial in the treatment of this life-threatening disease

UniPR1331: small Eph/ephrin antagonist beneficial in intestinal inflammation by interfering with type-B signaling

Eph receptors, comprising A and B classes, interact with cell-bound ephrins generating bidirectional signaling. Although mainly related to carcinogenesis and organogenesis, the role of Eph/ephrin system in inflammation is growingly acknowledged. Recently, we showed that EphA/ephrin-A proteins can modulate the acute inflammatory responses induced by mesenteric ischemia/reperfusion, while beneficial effects were granted by EphB4, acting as EphB/ephrin-B antagonist, in a murine model of Crohn’s disease (CD). Accordingly, we now aim to evaluate the effects of UniPR1331, a pan-Eph/ephrin antagonist, in TNBS-induced colitis and to ascertain whether UniPR1331 effects can be attributed to A- or B-type signaling interference. The potential anti-inflammatory action of UniPR1331 was compared to those of the recombinant proteins EphA2, a purported EphA/ephrin-A antagonist, and of ephrin-A1-Fc and EphA2-Fc, supposedly activating forward and reverse EphA/ephrin-A signaling, in murine TNBS-induced colitis and in stimulated cultured mononuclear splenocytes. UniPR1331 antagonized the inflammatory responses both in vivo, mimicking EphB4 protection, and in vitro; EphA/ephrin-A proteins were inactive or only weakly effective. Our findings represent a further proof-of-concept that blockade of EphB/ephrin-B signaling is a promising pharmacological strategy for CD management and highlight UniPR1331 as a novel drug candidate, seemingly working through the modulation of immune responses

N-tert-butyloxycarbonyl-Phe-Leu-Phe-Leu-Phe (BOC2) inhibits the angiogenic activity of heparin-binding growth factors.

The peptides N-tert-butyloxycarbonyl-Phe-Leu-Phe-Leu-Phe (BOC2) and BOC-Met-Leu-Phe (BOC1) are widely used antagonists of formyl peptide receptors (FPRs), BOC2 acting as an FPR1/FPR2 antagonist whereas BOC1 inhibits FPR1 only. Extensive investigations have been performed by using these FPR antagonists as a tool to assess the role of FPRs in physiological and pathological conditions. Based on previous observations from our laboratory, we assessed the possibility that BOC2 may exert also a direct inhibitory effect on the angiogenic activity of vascular endothelial growth factor-A (VEGF-A). Our data demonstrate that BOC2, but not BOC1, inhibits the angiogenic activity of heparin-binding VEGF-A165 with no effect on the activity of the non-heparin-binding VEGF-A121 isoform. Endothelial cell-based bioassays, surface plasmon resonance analysis, and computer modeling indicate that BOC2 may interact with the heparin-binding domain of VEGF-A165, thus competing for heparin interaction and preventing the binding of VEGF-A165 to tyrosine kinase receptor VEGFR2, its phosphorylation and downstream signaling. In addition, BOC2 inhibits the interaction of a variety of heparin-binding angiogenic growth factors with heparin, including fibroblast growth factor 2 (FGF2) whose angiogenic activity is blocked by the compound. Accordingly, BOC2 suppresses the angiogenic potential of human tumor cell lines that co-express VEGF-A and FGF2. Thus, BOC2 appears to act as a novel multi-heparin-binding growth factor antagonist. These findings caution about the interpretation of FPR-focusing experimental data obtained with this compound and set the basis for the design of novel BOC2-derived, FPR independent multi-target angiogenesis inhibitors

Conjugated polymers mediate intracellular Ca2+ signals in circulating endothelial colony forming cells through the reactive oxygen species-dependent activation of Transient Receptor Potential Vanilloid 1 (TRPV1)

Endothelial colony forming cells (ECFCs) represent the most suitable cellular substrate to induce revascularization of ischemic tissues. Recently, optical excitation of the light-sensitive conjugated polymer, regioregular Poly (3-hexyl-thiophene), rr-P3HT, was found to stimulate ECFC proliferation and tube formation by activating the non-selective cation channel, Transient Receptor Potential Vanilloid 1 (TRPV1). Herein, we adopted a multidisciplinary approach, ranging from intracellular Ca2+ imaging to pharmacological manipulation and genetic suppression of TRPV1 expression, to investigate the effects of photoexcitation on intracellular Ca2+ concentration ([Ca2+](i)) in circulating ECFCs plated on rr-P3HT thin films. Polymer-mediated optical excitation induced a long-lasting increase in [Ca2+](i) that could display an oscillatory pattern at shorter light stimuli. Pharmacological and genetic manipulation revealed that the Ca2+ response to light was triggered by extracellular Ca2+ entry through TRPV1, whose activation required the production of reactive oxygen species at the interface between rr-P3HT and the cell membrane. Light-induced TRPV1-mediated Ca2+ entry was able to evoke intracellular Ca2+ release from the endoplasmic reticulum through inositol-1,4,5-trisphosphate receptors, followed by store-operated Ca2+ entry on the plasma membrane. These data show that TRPV1 may serve as a decoder at the interface between rr-P3HT thin films and ECFCs to translate optical excitation in pro-angiogenic Ca2+ signals