Accelerated discovery of novel benzodiazepine ligands by experiment-guided virtual screening.

High throughput discovery of ligand scaffolds for target proteins can accelerate development of leads and drug candidates enormously. Here we describe an innovative workflow for the discovery of high affinity ligands for the benzodiazepine-binding site on the so far not crystallized mammalian GABAA receptors. The procedure includes chemical biology techniques that may be generally applied to other proteins. Prerequisites are a ligand that can be chemically modified with cysteine-reactive groups, knowledge of amino acid residues contributing to the drug-binding pocket, and crystal structures either of proteins homologous to the target protein or, better, of the target itself. Part of the protocol is virtual screening that without additional rounds of optimization in many cases results only in low affinity ligands, even when a target protein has been crystallized. Here we show how the integration of functional data into structure-based screening dramatically improves the performance of the virtual screening. Thus, lead compounds with 14 different scaffolds were identified on the basis of an updated structural model of the diazepam-bound state of the GABAA receptor. Some of these compounds show considerable preference for the α3β2γ2 GABAA receptor subtype.

Sol–Gel Coordination Chemistry: Building Catalysts from the Bottom-Up

The development of synthetic routes for the tailoring of efficient silica-based heterogeneous catalysts functionalized with coordination complexes or metallic nanoparticles has become a important goal in chemistry. Most of these techniques have been based on postsynthetic treatments of preformed silicas. Nevertheless, there is an emerging approach, so-called sol–gel coordination chemistry, based on co-condensation during the sol–gel preparation of the hybrid material of the corresponding complex or nanoparticle modified with terminal trialkoxysilane groups with a silica source (such as tetraethoxysilane) and in the presence of an adequate surfactant. This method leads to the production of new mesoporous metal complex-silica materials, with the metallic functionality incorporated homogeneously into the structure of the hybrid material, improving the stability of the coordination complex (which is protected by the silica network) and reducing the leaching of the active phase. This technique also offers the actual possibility of functionalizing silica or other metal oxides for a wider range of applications, such as photonics, sensing, and biochemical functions.

Microspheres for liver radiomicrospheres therapy and planning

Liver cancer accounts for nearly 10% of all cancers in the US. Intrahepatic Arterial Radiomicrosphere Therapy (RMT), also known as Selective Internal Radiation Treatment (SIRT), is one of the evolving treatment modalities. Successful patient clinical outcomes require suitable treatment planning followed by delivery of the microspheres for therapy. The production and in vitro evaluation of various polymers (PGCD, CHS and CHSg) microspheres for a RMT and RMT planning are described. Microparticles with a 30±10 µm size distribution were prepared by emulsion method. The in vitro half-life of the particles was determined in PBS buffer and porcine plasma and their potential application (treatment or treatment planning) established. Further, the fast degrading microspheres (≤ 48 hours in vitro half-life) were labeled with 68Ga and/or 99mTc as they are suitable for the imaging component of treatment planning, which is the primary emphasis of this dissertation. Labeling kinetics demonstrated that 68Ga-PGCD, 68Ga-CHSg and 68Ga-NOTA-CHSg can be labeled with more than 95% yield in 15 minutes; 99mTc-PGCD and 99mTc-CHSg can also be labeled with high yield within 15-30 minutes. In vitro stability after four hours was more than 90% in saline and PBS buffer for all of them. Experiments in reconstituted hemoglobin lysate were also performed. Two successful imaging (RMT planning) agents were found: 99mTc-CHSg and 68Ga-NOTA-CHSg. For the 99mTc-PGCD a successful perfusion image was obtained after 10 minutes, however the in vivo degradation was very fast (half-life), releasing the 99mTc from the lungs. Slow degrading CHS microparticles (> 21 days half-life) were modified with p-SCN-b-DOTA and labeled with 90 Y for production of 90Y-DOTA-CHS. Radiochemical purity was evaluated in vitro and in vivo showing more than 90% stability after 72 and 24 hours respectively. All agents were compared to their respective gold standards (99mTc-MAA for 68Ga-NOTA-CHSg and 99m Tc-CHSg; 90Y-SirTEX for 90Y-DOTA-CHS) showing superior in vivo stability. RMT and RMT planning agents (Therapy, PET and SPECT imaging) were designed and successfully evaluated in vitro and in vivo.

Microspheres for Liver Radiomicrospheres Therapy and Planning

Liver cancer accounts for nearly 10% of all cancers in the US. Intrahepatic Arterial Radiomicrosphere Therapy (RMT), also known as Selective Internal Radiation Treatment (SIRT), is one of the evolving treatment modalities. Successful patient clinical outcomes require suitable treatment planning followed by delivery of the microspheres for therapy. The production and in vitro evaluation of various polymers (PGCD, CHS and CHSg) microspheres for a RMT and RMT planning are described. Microparticles with a 30±10 µm size distribution were prepared by emulsion method. The in vitro half-life of the particles was determined in PBS buffer and porcine plasma and their potential application (treatment or treatment planning) established. Further, the fast degrading microspheres (≤ 48 hours in vitro half-life) were labeled with 68Ga and/or 99mTc as they are suitable for the imaging component of treatment planning, which is the primary emphasis of this dissertation. Labeling kinetics demonstrated that 68Ga-PGCD, 68Ga-CHSg and 68Ga-NOTA-CHSg can be labeled with more than 95% yield in 15 minutes; 99mTc-PGCD and 99mTc-CHSg can also be labeled with high yield within 15-30 minutes. In vitro stability after four hours was more than 90% in saline and PBS buffer for all of them. Experiments in reconstituted hemoglobin lysate were also performed. Two successful imaging (RMT planning) agents were found: 99mTc-CHSg and 68Ga-NOTA-CHSg. For the 99mTc-PGCD a successful perfusion image was obtained after 10 minutes, however the in vivo degradation was very fast (half-life), releasing the 99mTc from the lungs. Slow degrading CHS microparticles (> 21 days half-life) were modified with p-SCN-b-DOTA and labeled with 90Y for production of 90Y-DOTA-CHS. Radiochemical purity was evaluated in vitro and in vivo showing more than 90% stability after 72 and 24 hours respectively. All agents were compared to their respective gold standards (99mTc-MAA for 68Ga-NOTA-CHSg and 99mTc-CHSg; 90Y-SirTEX for 90Y-DOTA-CHS) showing superior in vivo stability. RMT and RMT planning agents (Therapy, PET and SPECT imaging) were designed and successfully evaluated in vitro and in vivo.

Polyaniline-based materials and nanocomposites: from energy storage to sensing applications

The research work described in this thesis concerns materials for both energy storage and sensoristics applications. Firstly, the synthesis and characterization of magnetite (Fe3O4) functionalyzed with [3-(2-propynylcarbamate)propyl]triethoxysilane (PPTEOS) capable to reduce the gold precursor chloroauric acid (HAuCl4) without the need of additional reducing or stabilising agents is described. These nanoparticles were tested to improve performances of symmetric capacitors based on polyaniline and graphite foil. Energy storage applications were investigated also during six months stay at EPFL University of Lausanne where an investigation about different tailored catalysts for Oxygen Evolution Reaction in a particular Redox Flow Battery was carried out. For what concerns sensing applications, new materials based on cellulose modified with polyaniline and poly(2-acrylamido-2-methyl-1-propanesulfonic acid) (PAAMPSA) were synthesized, characterized and applied to monitor pressure, humidity, heart rate and lastly, bread fermentation in collaboration with the University of Fribourg and Zurich. The characterizations of all the materials investigated compriseed numerous techniques such as infrared attenuated total reflectance spectroscopy (IR-ATR), thermogravimetric analysis (TGA), scanning and transmission electron microscopy (SEM and TEM), alongside linear and cyclic voltammetry (LSV and CV), electrochemical impedance spectroscopy (EIS) and chronoamperometric analyses.

Image analysis of modified cellulose fibers from sugarcane bagasse by zirconium oxychloride

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Study of adsorption and preconcentration by using a new silica organomodified with [3-(2,2′-dipyridylamine)propyl] groups

In this work, a silica surface chemically modified with [3-(2,2′-dipyridylamine)propyl] groups, named [3-(2,2′- dipyridylamine)propyl]silica (Si-Pr-DPA) was prepared, characterized, and evaluated for its heavy metal adsorption characteristics from aqueous solution. To our knowledge, we are the first authors who have reported the present modification. The material was characterized using infrared spectroscopy, SEM, and NMR 29Si and 13C solid state. Batch and column experiments were conducted to investigate for heavy metal removal from dilute aqueous solution by sorption onto Si-Pr-DPA. From a number of studies the affinity of various metal ions for the Si-Pr-DPA sorbent was determined to follow the order Fe(III) > Cr(III) >> Cu(II) > Cd(II) > Pb(II) > Ni(II). Two standard reference materials were used for checking the accuracy and precision of the method. The proposed method was successfully applied to the analysis of environmental samples. This ligand material has great advantage for adsorption of transition-metal ions from aqueous medium due to its high degree of organofunctionalization associated with the large adsorption capacity, reutilization possibility, and rapidity in reaching the equilibrium. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Síntese, caracterização e aplicação de celulose funcionalizada com o ligante P-aminobenzóico em pré- concentração de íons metálicos

Pós-graduação em Química - IQ

Effect of amino-terminated substrates onto surface properties of cellulose esters and their interaction with lectins

Films of cellulose acetate butyrate (CAB) and carboxymethylcellulose acetate butyrate (CMCAB) were deposited from ethyl acetate solutions onto bare silicon wafers (Si/SiO2) or amino-terminated surfaces (APS) by means of equilibrium adsorption. All surfaces were characterized by means of ellipsometry, atomic force microscopy (AFM) and contact angle measurements. The presence of amino groups on the support surface favored the adsorption of CAB and CMCAB, inducing the orientation almost polar groups to the surface and the exposition of alkyl group to the air. Such molecular orientation caused increase of the dispersive component of surface energy (gamma(d)(s)) and decrease of the polar component of surface energy (gamma(p)(s)) of cellulose esters in comparison to those values determined for films deposited onto bare Si/SiO2 wafers. Adsorption behavior of jacalin or concanavalin A onto CAB and CMCAB films was also investigated. The adsorbed amounts of lectins were more pronounced on cellulose esters with high (gamma(p)(s)) and total surface energy (gamma(t)(s)) values. (C) 2011 Elsevier B.V. All rights reserved.

Covalent attachment of Candida rugosa lipase on chemically modified hybrid matrix of polysiloxane-polyvinyl alcohol with different activating compounds

Candida rugosa lipase was immobilized by covalent binding on hybrid matrix of polysiloxane-polyvinyl alcohol chemically modified with different activating agents as glutaraldehyde, sodium metaperiodate and carbonyldiimidazole. The experimental results suggested that functional activating agents render different interactions between enzyme and support, producing consequently alterations in the optimal reaction conditions. Properties of the immobilized systems were assessed and their performance on hydrolytic and synthetic reactions were evaluated and compared with the free enzyme. In hydrolytic reactions using p-nitrophenyl palmitate as substrate all immobilized systems showed higher thermal stability and optima pH and temperature values in relation to the free lipase. Among the activating compounds, carbonyldiimidazole resulted in a total recovery of activity on the support and the highest thermal stability. For the butyl butyrate synthesis, the best performance (molar conversion of 95% and volumetric productivity of 2.33 g L-1 h(-1)) was attained with the lipase immobilized on POS-PVA activated with sodium metaperiodate. The properties of the support and immobilized derivatives were also evaluated by scanning electron microscopy (SEM), energy dispersive X-ray spectroscopies and chemical composition (FTIR). (c) 2007 Elsevier B.V. All rights reserved.

Thermoplastic starch modified during melt processing with organic acids: The effect of molar mass on thermal and mechanical properties

Thermoplastic starch (TPS) was modified with ascorbic acid and citric acid by melt processing of native starch with glycerol as plasticizer in an intensive batch mixer at 160 degrees C. It was found that the molar mass decreases with acid content and processing time causing the reduction in melting temperature (T(m)). As observed by the results of X-ray diffraction and DSC measurements, crystallinity was not changed by the reaction with organic acids. T(m) depression with falling molar mass was interpreted on the basis of the effect of concentration of end-chain units, which act as diluents. FTIR did not show any appreciable change in starch chemical compositions, leading to the conclusion that the main changes observed were produced by the variation in molar mass of the material. We demonstrated that it is possible to decrease melt viscosity without the need for more plasticizer thus avoiding side-effects such as an increase in water affinity or relevant changes in the dynamic mechanical properties. (C) 2010 Elsevier B.V. All rights reserved.

New modified electrochemical conductive paper support for BSA detection

Chemical sensors and biosensors are widely used to detect various kinds of protein target biomolecules. Molecularly Imprinted Polymers (MIPs) have raised great interest in this area, because these act as antibody-like recognition materials, with high affinity to the template molecule. Compared to natural antibodies, these are also of lower cost and higher stability. There are different types of supports used to carry MIP materials, mostly of these made of gold, favourably assembled on a Screen Printed Electrode (SPE) strategy. For this work a new kind of support for the sensing layer was developed: conductive paper. This support was made by modifying first cellulose paper with paraffin wax (to make it waterproof), and casting a carbon-ink on it afterwards, to turn it conductive. The SPAM approach previously reported in1 was employed herein to assemble to MIP sensing material on the conductive paper. The selected charged monomers were (vinylbenzyl) trimethlammonium chloride (positive charge) or vinylbenzoic acid (negative charge), used to generate binding positions with single-type charge (positive or negative). The non-specific binding area of the MIP layer was assembled by chronoamperometry-assisted polymerization (at 1 V, for 60, 120 or 180 seconds) of vinylbenzoate, cross-linked with ethylene glycol vinyl ether. The BSA biomolecules lying within the polymeric matrix were removed by Proteinase K action. All preparation stages of the MIP assembly were followed by FTIR, Raman spectroscopy and, electrochemical analysis. In general, the best results were obtained for longer polymerization times and positively charged binding sites (which was consistent with a negatively-charged protein under physiological pH, as BSA). Linear responses against BSA concentration ranged from 0.005 to 100 mg/mL, in PBS buffer standard solutions. The sensor was further calibrated in standard solutions that were prepared in synthetic or real urine, and the analytical response became more sensitive and stable. Compared to the literature, the detection capability of the developed device is better than most of the reported electrodes. Overall, the simplicity, low cost and good analytical performance of the BSA SPE device, prepared with positively charged binding positions, seems a suitable approach for practical application in clinical context. Further studies with real samples are required, as well as gathering with electronic-supporting devices to allow on-site readings.

Solid-phase synthesis and NMR studies of modified oligonucleotides forming triplex helix and of oligonucleopeptides mimicking the topoisomerase I-DNA covalent complex

Report for the scientific sojourn carried out at the Institut de Biologia Molecular de Barcelona of the CSIC –state agency – from april until september 2007. Topoisomerase I is an essential nuclear enzyme that modulates the topological status of DNA, facilitating DNA helix unwinding during replication and transcription. We have prepared the oligonucleotide-peptide conjugate Ac-NLeu-Asn-Tyr(p-3’TTCAGAAGC5’)-LeuC-CONH-(CH2)6-OH as model compound for NMR studies of the Topoisomerase I- DNA complex. Special attention was made on the synthetic aspects for the preparation of this challenging compound especially solid supports and protecting groups. The desired peptide was obtained although we did not achieve the amount of the conjugate needed for NMR studies. Most probably the low yield is due to the intrinsic sensitive to hydrolysis of the phosphate bond between oligonucleotide and tyrosine. We have started the synthesis and the structural characterization of oligonucleotides carrying intercalating compounds. At the present state we have obtained model duplex and quadruplex sequences modified with acridine and NMR studies are underway. In addition to this project we have successfully resolved the structure of a fusion peptide derived from hepatitis C virus envelope synthesized by the group of Dr. Haro and we have synthesized and started the characterization of a modified G-quadruplex.

Sílica quimicamente modificada com os grupos p-anisidina, p-fenitidina e p-fenilenodiamina usada como adsorvente para Pb2+, Cu2+, Cd2+ e Ni2+ em soluções aquosa e etanólica

Silica gel was chemically modified with the aromatic amines p-anisidine, p-phenytidine and p-phenylenediamine, using grafting reactions. The resulting modified silicas were characterized by infrared spectroscopy and N2 adsorption/desorption isotherms. The organic groups were covalently immobilized in a monolayer form. These modified silicas were investigated as adsorbents for Pb2+, Cu2+, Cd2+ and Ni2+ in aqueous and ethanol solutions. In a general way, the adsorption capacity values for all adsorbents presented the following sequence: Pb2+ >> Cu2+ @Cd2+ @ Ni2+. Adsorption studies for all adsorbents, in competitive medium, showed better selectivity for Cu2+ and Pb2+ in aqueous medium and for Pb2+ in ethanol solution. Desorption studies were carried out using HCl and HNO3 as eluents.

Dexamethasone and sodium carboxymethyl cellulose prevent postoperative intraperitoneal adhesions in rats

We aimed to evaluate the effects of the barrier agent sodium carboxymethyl cellulose (SCMC) with and without dexamethasone for the prevention of postoperative adhesion formation in a rat model of postoperative peritoneal adhesion. A total of 160 three-month old male and female Wistar rats underwent a laparotomy, and adhesions were induced by ileocecal abrasion. Rats were randomly assigned to 4 groups (n=40 each): group A, untreated; group B, treated with SCMC only; group C1, treated with SCMC + 3 mg dexamethasone, and group C2, treated with SCMC + 8 mg dexamethasone. After 12 days, adhesion formation and histopathological changes were compared. In groups A, B, C1, and C2, the mortality rates were 10, 5, 5, and 5%, respectively. In groups C1 and C2, the adhesions were filmy and easy to dissect and were milder compared with those in groups A and B. The total adhesion score in group C1 (3.38±0.49) was significantly lower than that of group B (6.01±0.57; P<0.01) or group A (8.01±0.67; P<0.05). There was no significant difference in adhesion formation between groups C1 and C2. Compared with groups A and B, groups C1 and C2 exhibited milder histopathological changes. SCMC in combination with dexamethasone can prevent adhesion formation and is a better barrier agent than SCMC alone. The safety and feasibility of SCMC in combination with dexamethasone to prevent adhesion formation after abdominal surgery warrants further clinical study.