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The Quest for Anticancer Vaccines: Deciphering the Fine-Epitope Specificity of Cancer-Related Monoclonal Antibodies by Combining Microarray Screening and Saturation Transfer Difference NMR, Coelho, Helena, Matsushita T., Artigas G., Hinou H., Cañada FJ, Lo-Man R., Leclerc C., Cabrita E. J., Jiménez-Barbero J., Nishimura S. - I., Garcia-Martín F., and Marcelo F. , J. Am. Chem. Soc., Volume 137, p.12438-12441, (2015)
A rational approach to sustainable CO2-capture by imidazolium ionic liquids: tuning CO2 solubility by cation alkyl branching, Corvo, Marta C., Sardinha João, Casimiro Teresa, Marin Graciane, Seferin Marcus, Einloft Sandra, Menezes Sonia C., Dupont Jairton, and Cabrita Eurico J. , Chem. Sus. Chem., Volume 8, p.1935-1946, (2015)
Rationalizing the role of the anion in CO2 capture and conversion using imidazolium-based ionic liquid modified mesoporous sílica, Aquino, Aline S., Bernard FL, Borges JV, Mafra Luis, Dalla Vecchia Felipe, Vieira MO, Ligabue R., Chaban VV, Cabrita E. J., and Einloft S. , RSC Advances, Volume 5, p.64220-64227, (2015)
Synthesis and evaluation of new benzimidazole-based COX inhibitors: a naproxen-like interaction detected by STD-NMR, Carvalho, L. C. R., Ribeiro D., Seixas R. S. G. R., Silva A. M. S., Nave M., Martins A. C., Erhardt S., Fernandes E., Cabrita E. J., and Marques M. M. B. , RSC Advances, Volume 5, p.49098-49109, (2015) AbstractWebsite

Non-steroidal anti-inflammatory drugs exert their pharmacological activity through inhibition of cyclooxygenase 1 and 2 (COX-1 and COX-2). Recent research suggests that a balanced inhibition of both COX-1 and COX-2 is the key to reduce the side-effects exhibited by COX inhibitors. We developed new benzimidazole-based compounds that showed a balanced COX inhibition, supported by molecular docking screening. The human whole blood assays demonstrated that the ester derivatives were potent inhibitors. Competitive saturation transfer difference (STD)-NMR experiments, in the presence of COX-2, using naproxen and diclofenac demonstrated that ester derivatives do not compete with diclofenac for the same binding site, but compete with the allosteric inhibitor naproxen. Combination of NMR spectroscopy with molecular docking has permitted us to detect a new naproxen-like inhibitor, which could be used for future drug development.

Assessing diffusion in enzyme loaded sol–gel matrices, Barreira, Gustavo, Ferreira Ana S. D., Vidinha Pedro, Cabral Joaquim M. S., Martinho José M. G., Lima João Carlos, Cabrita Eurico J., and Barreiros Susana , RSC Advances, Volume 4, p.25099-25105, (2014) AbstractWebsite

Pulsed field gradient spin echo high resolution magic angle spinning nuclear magnetic resonance spectroscopy is a powerful technique to characterize confined biosystems. We used this approach to assess the diffusion of solvent and reaction species within sol–gel matrices differing in enzyme loading.

Biochemical, Stabilization and Crystallization Studies on a Molecular Chaperone (PaoD) Involved in the Maturation of Molybdoenzymes., Otelo-Cardoso, AR, Schwuchow V., Rodrigues D., Cabrita E. J., Leimkühler S., Romão MJ, and Santos-Silva T. , PLoS One, Volume 9, p.e87295 , (2014) AbstractWebsite

Molybdenum and tungsten enzymes require specific chaperones for folding and cofactor insertion. PaoD is the chaperone of the periplasmic aldehyde oxidoreductase PaoABC. It is the last gene in the paoABCD operon in Escherichia coli and its presence is crucial for obtaining mature enzyme. PaoD is an unstable, 35 kDa, protein. Our biochemical studies showed that it is a dimer in solution with a tendency to form large aggregates, especially after freezing/thawing cycles. In order to improve stability, PaoD was thawed in the presence of two ionic liquids [C4mim]Cl and [C2OHmim]PF6 and no protein precipitation was observed. This allowed protein concentration and crystallization using polyethylene glycol or ammonium sulfate as precipitating agents. Saturation transfer difference – nuclear magnetic resonance (STD-NMR) experiments have also been performed in order to investigate the effect of the ionic liquids in the stabilization process, showing a clear interaction between the acidic ring protons of the cation and, most likely, negatively charged residues at the protein surface. DLS assays also show a reduction of the overall size of the protein aggregates in presence of ionic liquids. Furthermore, cofactor binding studies on PaoD showed that the protein is able to discriminate between molybdenum and tungsten bound to the molybdenum cofactor, since only a Mo-MPT form of the cofactor remained bound to PaoD.

Delineating binding modes of Gal/GalNAc and structural elements of the molecular recognition of tumor-associated mucin glycopeptides by the human macrophage galactose-type lectin, Marcelo, Filipa, Garcia-Martin Fayna, Matsushita Takahiko, Sardinha João, Coelho Helena, Oude-Vrielink Anneloes, Koller Christiane, André Sabine, Cabrita Eurico J., Gabius Hans-Joachim, Nishimura Shin-Ichiro, Jiménez-Barbero Jesús, and Cañada Javier F. , Chem. Eur. J., Volume in press, (2014) Abstract

The human macrophage galactose-type lectin (hMGL) is a key physiological receptor for the carcinoma-associated Tn antigen (GalNAc-α-1-O-Ser/Thr) in mucins. We herein report NMR- and modeling-based data on the molecular recognition features of synthetic Tn-bearing glycopeptides by hMGL. Cognate epitopes on the sugar and matching key amino acids involved in the interaction have been identified by saturation transfer difference (STD) NMR spectroscopy. Only the amino acids close to the glycosylation site in the peptides are involved in lectin contact. Moreover, control experiments with non-glycosylated MUC1 peptides unequivocally showed that the sugar residue is essential for hMGL binding, as is Ca2+. The dissociation constants (Kd) have been estimated by STD titrations and/or STD competition experiments and show that Gal was a poor binder for hMGL, with a Kd in the mM range, while GalNAc and MUC1 Tn-glycopetides reached Kd values in the lower μM range. STD-based results suggested a distinct interacting epitope for the two monosaccharides. NMR data have been complemented with molecular dynamics simulations and Corcema- ST to establish a 3D view on the molecular recognition process between Gal, GalNAc and the Tn-presenting glycopeptides and hMGL. Gal and GalNAc have a dual binding mode with opposite trend of the main interaction pattern and the differences in affinity can be explained by additional hydrogen bonds and CH-π contacts involving exclusively the NHAc moiety.

Epitope mapping of imidazolium cations in ionic liquid–protein interactions unveils the balance between hydrophobicity and electrostatics towards protein destabilisation, Silva, Micael, Figueiredo Angelo Miguel, and Cabrita Eurico J. , Phys. Chem. Chem. Phys. , Volume in press, (2014) Abstract

We investigated imidazolium-based ionic liquid (IL) interactions with human serum albumin (HSA) to discern the level of cation interactions towards protein stability. STD-NMR spectroscopy was used to observe the imidazolium IL protons involved in direct binding and to identify the interactions responsible for changes in Tm as accessed by differential scanning calorimetry (DSC). Cations influence protein stability less than anions but still significantly. It was found that longer alkyl side chains of imidazolium- based ILs (more hydrophobic) are associated with a higher destabilisation effect on HSA than short-alkyl groups (less hydrophobic). The reason for such destabilisation lies on the increased surface contact area of the cation with the protein, particularly on the hydrophobic contacts promoted by the terminus of the alkyl chain. The relevance of the hydrophobic contacts is clearly demonstrated by the introduction of a polar moiety in the alkyl chain: a methoxy or alcohol group. Such structural modification reduces the degree of hydrophobic contacts with HSA explaining the lesser extent of protein destabilisation when compared to longer alkyl side chain groups: above [C2mim]+. Competition STD-NMR experiments using [C2mim]+, [C4mim]+ and [C2OHmim]+ also validate the importance of the hydrophobic interactions. The combined effect of cation and anion interactions was explored using 35Cl NMR. Such experiments show that the nature of the cation has no influence on the anion–protein contacts, still the nature of the anion modulates the cation–protein interaction. Herein we propose that more destabilising anions are likely to be a result of a partial contribution from the cation as a direct consequence of the different levels of interaction (cation–anion pair and cation–protein).

Inhibition of LOX by flavonoids: a structure-activity relationship study., Ribeiro, D., Freitas M., Tomé SM, Silva AM, Porto G., Cabrita E. J., Marques M. M., and Fernandes E. , European Journal of Medicinal Chemistry, Volume 72, p.137-145, (2014) AbstractWebsite

The lipoxygenase (LOX) products have been identified as mediators of a series of inflammatory diseases, namely rheumatoid arthritis, inflammatory bowel disease, psoriasis, allergic rhinitis, atherosclerosis and certain types of cancer. Hence, LOX inhibitors are of interest for the modulation of these phenomena and resolution of the inflammatory processes. During LOX activity, peroxyl radical complexes are part of the reaction and may function as sources of free radicals. Thus antioxidants, such as flavonoids, capable of inhibiting lipid peroxidation and scavenging free radicals, may act as LOX inhibitors. The aim of this work was to assess the structure–activity relationship among a series of flavonoids concerning 5-LOX inhibition, through a systematic study of the inhibition of the formation of LTB4 in human neutrophils. The type of inhibition of the flavonoids was further studied using soybean LOX, type I, and Saturation Transfer Difference 1H NMR (STD-1H NMR) was used to characterize the binding epitopes of the compounds to LOX-1. The obtained results reinforce flavonoids as effective inhibitors of LTB4 production in human neutrophils. It was also possible to establish a structure/activity relationship for the inhibitory activity and the type of inhibition.

Ion Jelly Conductive Properties Using Dicyanamide-Based Ionic Liquids, Carvalho, T., Augusto V., Rocha A., Lourenco N. M. T., Correia N. T., Barreiros S., Vidinha P., Cabrita E. J., and Dionisio M. , Journal of Physical Chemistry B, Volume 118, Issue 31, p.9445-59, (2014) AbstractWebsite

The thermal behavior and transport properties of several ion jellys (IJs), a composite that results from the combination of gelatin with an ionic liquid (IL), were investigated by dielectric relaxation spectroscopy (DRS), differential scanning calorimetry (DSC), and pulsed field gradient nuclear magnetic resonance spectroscopy (PFG NMR). Four different ILs containing the dicyanamide anion were used: 1-butyl-3-methylimidazolium dicyanamide (BMIMDCA), 1-ethyl-3-methylimidazolium dicyanamide (EMIMDCA), 1-butyl-1-methylpyrrolidinium dicyanamide (BMPyrDCA), and 1-butylpyridinium dicyanamide (BPyDCA); the bulk ILs were also investigated for comparison. A glass transition was detected by DSC for all materials, ILs and IJs, allowing them to be classified as glass formers. Additionally, an increase in the glass transition temperature upon dehydration was observed with a greater extent for IJs, attributed to a greater hindrance imposed by the gelatin matrix after water removal, rendering the IL less mobile. While crystallization is observed for some ILs with negligible water content, it was never detected for any IJ upon thermal cycling, which persist always as fully amorphous materials. From DRS measurements, conductivity and diffusion coefficients for both cations (D+) and anions (D–) were extracted. D+ values obtained by DRS reveal excellent agreement with those obtained from PFG NMR direct measurements, obeying the same VFTH equation over a large temperature range (ΔT ≈ 150 K) within which D+ varies around 10 decades. At temperatures close to room temperature, the IJs exhibit D values comparable to the most hydrated (9%) ILs. The IJ derived from EMIMDCA possesses the highest conductivity and diffusion coefficient, respectively, 10–2 S·cm–1 and 10–10 m2·s–1. For BMPyrDCA the relaxational behavior was analyzed through the complex permittivity and modulus formalism allowing the assignment of the detected secondary relaxation to a Johari–Goldstein process. Besides the relevant information on the more fundamental nature providing physicochemical details on ILs behavior, new doorways are opened for practical applications by using IJ as a strategy to produce novel and stable electrolytes for different electrochemical devices.

Binding analysis between l-histidine immobilized and oligonucleotides by SPR and NMR, Cruz, Carla, Santos Sandra D., Cabrita Eurico J., and Queiroz João A. , International Journal of Biological Macromolecules, Volume 56, p.175-180, (2013) AbstractWebsite

Saturation transfer difference (STD) NMR technique and surface plasmon resonance (SPR) are used to study amino acid affinity supports–nucleotides interactions with l-histidine amino acid immobilized on a surface as model support. We have immobilized l-histidine ligand on a carboxymethyldextran- modified gold surface intended for surface plasmon resonance and we analyze the binding profiles of synthetic polynucleotides (1–6 base, sugar and backbone) by determining the equilibrium dissociation constant (KD). The SPR binding profile (square-shaped) is identical for all the complexes and the highest binding affinity can be found for polyA6 followed by polyG6 . As expected, the 5′ -mononucleotides have the lowest affinity. To further study the structural aspects of the interaction we investigate the polynucleotide binding preferences to l-histidine chromatography support by STD-NMR spectroscopy. These results revealed that an increase in the number of bases and backbone to 6 units leads to more contacts with the support, where the main driving force for the interaction with polynucleotides are through the base, except for polyC6 , which is mainly through sugar-phosphate backbone. Therefore, the combination of SPR measurements with STD-NMR technique allowed to establish fine details of the molecular recognition process involved in amino acid affinity supports–nucleotides complexes.

Molecular Recognition of Rosmarinic Acid from Salvia sclareoides Extracts by Acetylcholinesterase: A New Binding Site Detected by NMR Spectroscopy, Marcelo, Filipa, Dias Catarina, Madeira Paulo J., Jorge Tiago, Florêncio Helena M., Canada Javier F., Cabrita Eurico J., Jiménez-Barbero Jésus, and Rauter Amelia P. , Chemistry: A European Journal, Volume 19, p.6641-6649, (2013) AbstractWebsite

Acetylcholinesterase (AChE) inhibition is one of the most currently available therapies for the management of Alzheimer’s disease (AD) symptoms. In this context, NMR spectroscopy binding studies were accomplished to explain the inhibition of AChE activity by Salvia sclareoides extracts. HPLC-MS analyses of the acetone, butanol and water extracts eluted with methanol and acidified water showed that rosmarinic acid is present in all the studied samples and is a major constituent of butanol and water extracts. Moreover, luteolin 4′-O-glucoside, luteolin 3′,7-di-O-glucoside and luteolin 7-O-(6′′-O-acetylglucoside) were identified by MS2 and MS3 data acquired during the LC-MSn runs. Quantification of rosmarinic acid by HPLC with diode-array detection (DAD) showed that the butanol extract is the richest one in this component (134 μg mg−1 extract). Saturation transfer difference (STD) NMR spectroscopy binding experiments of S. sclareoides crude extracts in the presence of AChE in buffer solution determined rosmarinic acid as the only explicit binder for AChE. Furthermore, the binding epitope and the AChE-bound conformation of rosmarinic acid were further elucidated by STD and transferred NOE effect (trNOESY) experiments. As a control, NMR spectroscopy binding experiments were also carried out with pure rosmarinic acid, thus confirming the specific interaction and inhibition of this compound against AChE. The binding site of AChE for rosmarinic acid was also investigated by STD-based competition binding experiments using Donepezil, a drug currently used to treat AD, as a reference. These competition experiments demonstrated that rosmarinic acid does not compete with Donepezil for the same binding site. A 3D model of the molecular complex has been proposed. Therefore, the combination of the NMR spectroscopy based data with molecular modelling has permitted us to detect a new binding site in AChE, which could be used for future drug development.

NMR Solution Structure and SRP54M predicted interaction of the N-Terminal sequence (1-30) of the ovine Doppel protein, Pimenta, Jorge, Viegas Aldino, Sardinha João, Martins Ivo C., Cabrita Eurico J., Fontes Carlos M. G. A., Prates Jose A. M., and Pereira Rosa M. L. N. , Peptides, Volume 49, p.32-40, (2013) AbstractWebsite

Prion protein (PrPC) biosynthesis involves a multi-step process that includes translation and post-translational modifications. While PrP has been widely investigated, for the homolog Doppel (Dpl), limited knowledge is available. In this study, we focused on a vital step of eukaryotic protein biosynthesis: targeting by the signal recognition particle (SRP). Taking the ovine Dpl (OvDpl(1-30)) peptide as a template, we studied its behavior in two different hydrophobic environments using CD and NMR spectroscopy. In both trifluoroethanol (TFE) and dihexanoyl-sn-glycero-3-phosphatidylcholine (DHPC), the OvDpl(1-30) peptide revealed to fold in an alpha-helical conformation with a well-defined central region extending from residue Cys8 until Ser22. The NMR structure was subsequently included in a computational docking complex with the conserved M-domain of SRP54 protein (SRP54M), and further compared with the N-terminal structures of mouse Dpl and bovine PrPC proteins. This allowed the determination of (i) common predicted N-terminal/SRP54M polar contacts (Asp331, Gln335, Glu365 and Lys432) and (ii) different N–C orientations between prion and Dpl peptides at the SRP54M hydrophobic groove, that are in agreement with each peptide electrostatic potential. Together, these findings provide new insights into the biosynthesis of prion-like proteins. Besides they also show the role of protein conformational switches in signalization toward the endoplasmic membrane, a key event of major significance in the cell cycle. They are thus of general applicability to the study of the biological function of prion-like as well as other proteins.

Protein destabilisation in ionic liquids: the role of preferential interactions in denaturation, Figueiredo, Angelo Miguel, Sardinha João, Moore Geoffrey R., and Cabrita Eurico J. , Phys. Chem. Chem. Phys., Issue 15, p.19632-19643, (2013) AbstractWebsite

The preferential binding of anions and cations in aqueous solutions of the ionic liquids (ILs) 1-butyl- 3-methylimidazolium ([C4mim]+) and 1-ethyl-3-methylimidazolium ([C2mim]+) chloride and dicyanamide (dca-) with the small alpha-helical protein Im7 was investigated using a combination of differential scanning calorimetry, NMR spectroscopy and molecular dynamics (MD) simulations. Our results show that direct ion interactions are crucial to understand the effects of ILs on the stability of proteins and that an anion effect is dominant. We show that the binding of weakly hydrated anions to positively charged or polar residues leads to the partial dehydration of the backbone groups, and is critical to control stability, explaining why dca- is more denaturing than Cl-. Direct cation–protein interactions also mediate stability; cation size and hydrophobicity are relevant to account for destabilisation as shown by the effect of [C4mim]+ compared to [C2mim]+. The specificity in the interaction of IL ions with protein residues established by weak favourable interactions is confirmed by NMR chemical shift perturbation, amide hydrogen exchange data and MD simulations. Differences in specificity are due to the balance of interaction established between ion pairs and ion-solvent that determine the type of residues affected. When the interaction of both cation and anion with the protein is strong the net result is similar to a non-specific interaction, leading ultimately to unfolding. Since the nature of the ions is a determinant of the level of interaction with the protein towards denaturation or stabilisation, ILs offer a unique possibility to modulate protein stabilisation or even folding events.

Shaping the molecular assemblies of native and alkali- modified agars in dilute and concentrated aqueous media via microwave-assisted extraction, Sousa, Ana M. M., Borges João, Silva Fernando, Ramos Ana M., Cabrita Eurico J., and Gonçalves Maria Pilar , Soft Matter, Volume 9, p.3131-3139, (2013) AbstractWebsite

The use of agar-based biomaterials for the development of emerging areas, such as tissue engineering or ‘smart materials’ production has recently gained great interest. Understanding how these gel-forming polysaccharides self-organise in aqueous media and how these associations can be tuned to meet the specific needs of each application is thus of great relevance. As an extension of previous pioneering research concerning the application of the microwave-assisted extraction (MAE) technique in the recovery of native (NA) and alkali-modified (AA) agars, this article focuses on the different molecular assemblies assumed by these novel NA and AA when using different MAE routes. The molecular architectures in dilute (5, 10, 50 and 100 mg mL1) and concentrated (1.5% (w/w)) aqueous media were imaged by AFM and cryoSEM, respectively. Relevant structural and physicochemical properties were investigated to support the microscopic data. Different extraction routes led to polysaccharides with unique properties, which in turn resulted in different molecular assemblies. Even at 5 mg mL1, AFM images included individual fibers, cyclic segments, aggregates and local networks. At higher polymer concentrations, the structures further aggregated forming multilayer polymeric networks for AA. The more compact and denser 3D networks of AA, imaged by cryoSEM, and their higher resistance to large deformations matched the 2D-shapes observed by AFM. Depending on the nature of the AA chains, homogeneous or heterogeneous growth of assemblies was seen during network formation. The obtained results support well the view of double helix formation followed by intensive double helix association proposed for agar gelation.

Solution Structure, Dynamics and Binding Studies of a Family 11 Carbohydrate-Binding Module from Clostridium thermocellum (CtCBM11), Viegas, Aldino, Sardinha João, Duarte Daniel F., Carvalho Ana Luisa, Fontes Carlos M. G. A., Romao Maria Joao, Macedo Anjos L., and Cabrita Eurico J. , Biochemical Journal, Volume 451, p.289-300, (2013) AbstractWebsite

Non-catalytic cellulosomal carbohydrate-binding modules (CBMs) are responsible for increasing the catalytic efficiency of cellulosic enzymes by selectively putting the substrate (a wide range of poly- and oligosaccharides) and enzyme into close contact. In the present work we carried out an atomistic rationalization of the molecular determinants of ligand specificity of a family 11 CBM from thermophilic C. thermocellum (CtCBM11), based on a NMR and molecular modeling approach. We have determined the NMR solution structure of CtCBM11 at 25 and 50 ºC and derived information on the residues of the protein involved in ligand recognition and on the influence of the length of the saccharide chain on binding. We obtained models of the CtCBM11/cellohexaose and CtCBM11/cellotetraose complexes by docking in accordance with the NMR experimental data. Specific ligand/protein CH-π and Van der Waals interactions were found to be determinant for the stability of the complexes and for defining specificity. Using the order parameters derived from backbone dynamics analysis in the presence and absence of ligand and at 25 and 50 ºC, we determined that the protein’s backbone conformational entropy is slightly positive. This data in combination with the negative binding entropy calculated from ITC studies supports a selection mechanism where a rigid protein selects a defined oligosaccharide conformation.

Solvation of CO2 in [C4mim][BF4] and [C4mim][PF6] ionic liquids revealed by High Pressure NMR, Corvo, Marta C., Sardinha João, Menezes Sonia C., Einloft Sandra, Seferin Marcus, Dupont Jairton, Casimiro Teresa, and Cabrita Eurico J. , Angewandte Chemie International Edition, Volume 49, Issue 52, p.13024-13027, (2013) Website
Synthesis and characterization of novel γ-induced porous PHEMA–IL composites, Casimiro, MH, Corvo Marta C., Ramos A. M., Cabrita E. J., Ramos A. M., and Ferreira LM , Materials Chemistry and Physics, Volume 138, Issue 1, p.11-16, (2013) AbstractWebsite

A novel porous polymer-ionic liquid composite with poly(2-hydroxyethyl methacrylate) (PHEMA) and 1-butyl-3-methylimidazolium hexafluorophosphate (BMIPF6) has been synthesized by γ-irradiation without heat or chemical initiators. The products can be reversibly converted into organogels. The composites are potential candidates for electrochemical applications. The use of γ-radiation can be a simple and versatile alternative way to obtain these materials.

Antifungals on paper conservation: An overview , Sequeira, Sílvia, Cabrita Eurico J., and Macedo Filomena M. , International Biodeterioration & Biodegradation, Volume 74, p.67-84, (2012) Abstract

Since its invention, paper has become one of the main carriers of our cultural, scientific, political, economic and historical information. Given the importance of this material, its preservation is a matter of great interest. Paper can be deteriorated due to physical, chemical and biological agents. Within microorganisms, fungi are the major paper biodeteriogens. Throughout history, several methods have been used to prevent and stop fungal deterioration on paper based materials. In this work we present a review of the main chemical and physical methods used to avoid fungal paper biodeterioration until nowadays and also of some new approaches tested recently. The advantages and disadvantages of these methods are discussed as well as their health effects. Studies regarding antifungal compositions, methods of application, performance and effects on the treated materials are also presented with the aim of providing a clear set of conclusions on the topic. (C) 2012 Elsevier Ltd. All rights reserved.

Thymus mastichina: Chemical Constituents and their Anti-cancer Activity , Gordo, Joana, Máximo Patrícia, Cabrita Eurico, Lourenço Ana, Oliva Abel, Almeida Joana, Filipe Mariana, Cruz Pedro, Barcia Rita, Santos Miguel, and Cruz Helder , Natural Product Communications, Volume 7, Issue 11, p.1491-1494, (2012)
Indole based cyclooxygenase inhibitors: synthesis, biological evaluation, docking and NMR screening, Estevão, Mónica S., Carvalho Luísa C. R., Freitas Marisa, Gomes Ana, Viegas Aldino, Manso João, Erhadrt Stefan, Cabrita Eurico J., and Marques Maria Manuel B. , European Journal of Medicinal Chemistry, Volume 54, p.823-833, (2012) Abstract

The close structural similarity between the two cyclooxygenase (COXs) isoforms and the absence of selective inhibitors without side effects continues to stimulate the development of novel approaches towards selective anti-inflammatory drugs. In the present study a small library of new indolic compounds involving two different substitutions patterns at the indole scaffold was synthesized. In order to establish a relation between the spatial distribution of known functional groups related with inhibitory activity, two substitution patterns were explored: one with substituents at N-1, C-3, C-5 positions and another at C-2, C-3 and C5 positions. Accordingly, indole positions C-5, C-3 and N-1 were substituted with: sulfonamide or methylsulfone at C-5, p-halo-benzyl group at C-3, and an alkyl chain with a trifluoromethyl group at N-1. Alternatively, a p-halo-benzyl group was introduced at C-2, leaving the indolic nitrogen free. Inhibitory studies were performed and the activity results obtained against both COXs isoforms were rationalized based on docking and NMR studies. Docking studies show that dialkyation at C-2 and C-3 favors a binding with an orientation similar to that of the known selective inhibitor SC-558. From the tested compounds, this substitution pattern is correlated with the highest inhibitory activity and selectivity: 70% COX-2 inhibition at 50 M, and low COX-1 inhibition (18±9%). Additionally, Saturation Transfer Difference NMR experiments reveal different interaction patterns with both COXs isoforms that may be related with different orientations of the sulfonamide group in the binding pocket. Despite the moderated inhibitory activities found, this study represents an innovative approach towards COXs inhibitory activity rationalization and to the design of anti-inflammatory drugs.

Platinated DNA Affects Zinc Finger Conformation. The Interaction of a Platinated Single-Stranded Oligonucleotide and the C-terminal Zinc Finger of the Nucleocapsid Protein HIVNCp7, Quintal, Susana Maria, Viegas Aldino, Erhardt Stefan, Cabrita Eurico J., and Farrell Nicholas P. , Biochemistry, Volume 51, p.1752-1761, (2012) AbstractWebsite

This paper describes for the first time the intimate molecular details of the association between a platinated oligonucleotide and a zinc-finger peptide. Site-specific platination of the guanine in a ss hexanucleotide gave {[Pt(dien)d(5’-TACGCC-3’)], Pt(dien)(6-mer)}, II, characterized by mass spectrometry and 1H-NMR spectroscopy. The work extends the study of platinum-nucleobase complex-zinc finger interactions using small molecules such as [Pt(dien)(9-EtGua)]2+, I . The structure of the (34-52) C-terminal finger of the HIV nucleocapsid protein HIVNCp7 (ZF1) was characterized by 1H-NMR spectroscopy and compared with that of the N-terminal single finger and the 2-finger “intact” NCp7. Interaction of II with ZF1 results in significant changes in comparison to the “free” uncomplexed hexanucleotide – the major shifts occur for Trp37 resonances are broadened and shifted upfield and other major shifts are for Gln45 (H21, H3, Q), Met46 (NH, H2), Lys47 (NH, Q) and Glu50 (H2, H3). The Zn-Cys/His chemical shifts show only marginal deviations. The solution structure of ZF1, the 6-mer/ZF1 and II/ZF1 adducts were calculated from the NOESY-derived distance constraints. The DNA position in II/ZF1 is completely different than in the absence of platinum. Major differences are the appearance of new Met46-Cyt6H5 and Trp37-Cyt5H5 contacts but severe weakening of the Trp37-Gua4 contact, attributed to the steric effects caused by Gua4 platination, accompanied by a change in the position of the aromatic ring. The results demonstrate the feasibility of targetting specific ZF motifs with DNA-tethered coordination compounds, such as Pt compounds and Co-macrocycles – with implications for drug targetting and indeed the intimate mechansims of DNA repair of platinated DNA.

The Prion-like Protein Doppel Enhances Ovine Spermatozoa Fertilizing Ability, Pimenta, J., Dias FMV, Marques C. C., Baptista M. C., Vasques M. I., Horta A. E. M., Barbas J. P., Soares R., Mesquita P., Cabrita E., Fontes CMGA, Prates J. A., and Pereira R. M. , Reproduction in Domestic Animals, Volume 47, Issue 2, p.196-202, (2012) Abstract

The function of prion-like protein Doppel was suggested to be related to male fertility. In this study, the importance of ovine Doppel polypeptide on spermatozoa capacitation and fertilization was evaluated. After refolding, recombinant Doppel (rDpl) was supplemented with different concentrations (40, 80 or 190 ng/ml) to ovine spermatozoa during the capacitation process. In experiment 1, post-thawed ovine spermatozoa were incubated with different concentrations of rDpl during 1 h for swim-up, and changes in sperm motility, concentration, vigour, viability and capacitation were monitored (10 replicates). In experiment 2, the fertilization ability of post-swim-up spermatozoa incubated as above was tested through heterologous fertilization of bovine in vitro matured oocytes (n = 423, three replicates). Regardless of dosage, rDpl improved (p = 0.03) spermatozoa viability. Sperm individual motility and vigour were the highest (p = 0.04) for the group receiving 190 ng/ml rDpl. Sperm supplemented with the highest doses of rDpl achieved higher (p = 0.02) fertilization rates (56.0 +/- 3.0%) than control (39.1 +/- 2.2%) and 40 ng/ml rDpl (39.8 +/- 2.7%). Preliminary data suggest that Doppel protein may enhance in vitro spermatozoa fertilizing ability.

Structural, Physical, and Chemical Modifications Induced by Microwave Heating on Native Agar-like Galactans, Sousa, Ana M. M., Morais Simone, Abreu Maria H., Pereira Rui, Sousa-Pinto Isabel, Cabrita Eurico J., Delerue-Matos Cristina, and Gonca̧lves Maria Pilar , Jornal of Agricultural and Food Chemistry , Volume 60, p.4977-4985, (2012) Abstract

Native agars from Gracilaria vermiculophylla produced in sustainable aquaculture systems (IMTA) were extracted under conventional (TWE) and microwave (MAE) heating. The optimal extracts from both processes were compared in terms of their properties. The agars’ structure was further investigated through Fourier transform infrared and NMR spectroscopy. Both samples showed a regular structure with an identical backbone, β-D-galactose (G) and 3,6-anhydro-α-L-galactose (LA) units; a considerable degree of methylation was found at C6 of the G units and, to a lesser extent, at C2 of the LA residues. The methylation degree in the G units was lower for MAEopt agar; the sulfate content was also reduced. MAE led to higher agar recoveries with drastic extraction time and solvent volume reductions. Two times lower values of [η] and Mv obtained for the MAEopt sample indicate substantial depolymerization of the polysaccharide backbone; this was reflected in its gelling properties; yet it was clearly appropriate for commercial application in soft-texture food products.

Understanding the Ion Jelly Conductivity Mechanism, Carvalho, T., Augusto V., Brás A. R., Lourenço N. M. T., Afonso CAM, Barreiros S., Correia N. T., Vidinha P., Cabrita E. J., Dionísio M., and Roling B. , Journal of Physical Chemistry B, Volume 116, p.2664-2676, (2012) Abstract

The properties of the light flexible device, ion jelly, which combines gelatin with an ionic liquid (IL) were recently reported being promising to develop safe and highly conductive electrolytes. This article aims for the understanding of the ion jelly conductive mechanism using dielectric relaxation spectroscopy (DRS) in the frequency range 10−1−106 Hz; the study was complemented with differential scanning calorimetry (DSC) and pulse field gradient nuclear magnetic resonance (PFG NMR) spectroscopy. The room temperature ionic liquid 1-butyl-3-methylimmidazolium dicyanamide (BMIMDCA) used as received (1.9% w/w water content) and with 6.6% (w/w) of water content and two ion jellies with two different ratios BMIMDCA/gelatin/water % (w/w), IJ1 (41.1/46.7/12.2) and IJ3 (67.8/25.6/6.6), have been characterized. A glass transition was detected by DSC for all materials allowing for classifying them as glass formers. For the ionic liquid, it was observed that the glass transition temperature decreases with the increase of water content. While in subsequent calorimetric runs crystallization was observed for BMIMDCA with negligible water content, no crystallization was detected for any of the ion jelly materials upon themal cycling. To the dielectric spectra of all tested materials, both dipolar relaxation and conductivity contribute; at the lowest frequencies, electrode and interfacial polarization highly dominate. Conductivity, which manifests much more intensity relative to dipolar reorientations, strongly evidences subdiffusive ion dynamics at high frequencies. From dielectric measures, transport properties as mobility and diffusion coefficients were extracted. Data treatment was carried out in order to deconvolute the average diffusion coefficients estimated from dielectric data in its individual contributions of cations (D+) and anions (D−). The D+ values thus obtained for IJ3, the ion jelly with the highest IL/gelatin ratio, cover a large temperature range up to room temperature and revealed excellent agreement with direct measurements from PFG NMR, obeying to the same VFT equation. For BMIMDCA6.6%water, which has the same water amount as IJ3, the diffusion coefficients were only estimated from DRS measurements over a limited temperature range; however, a single VFT equation describes both DRS and PFG NMR data. Moreover, it was found that the diffusion coefficients and mobility are similar for the ionic liquid and IJ3, which points to a role of both water and gelatin weakening the contact ion pair, facilitating the translational motion of ions and promoting its dissociation; nevertheless, it is conceivable that a critical composition of gelatin that leads to those properties. The VFT temperature dependence observed for the conductivity was found to be determined by a similar dependence of the mobility. Both conductivity and segmental motion revealed to be correlated as inferred by the relatively low values of the decoupling indexes. The obtained results show that ion jelly could be in fact a very promising material to design novel electrolytes for different electrochemical devices, having a performance close to the IL but presenting an additional stability regarding electrical measurements and resistance against crystallization relative to the bulk ionic liquid.